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C++ Class: CigarRoller

2,293 bytes removed, 12:00, 2 February 2017
Cigar
= Cigar=
This class is part of [[C++ LibrarylibStatGen: libStatGengeneral]].
The purpose of this class is to provide utilities for processing CIGARs. It has read-only operators that do not allow modification to the class other than for lazy-evaluation.
See: [http://www.sph.umich.edu/csg/mktrost/doxygen/current/classCigar.html http://www.sph.umich.edu/csg/mktrost/doxygen/current/classCigar.html] for documentation.
The static methods are helpful for determining information about the operator.
See [[C++ Class: CigarRoller#Determining the Number of Reference and Read/Query Overlaps|Determining the Number of Reference and Read/Query Overlaps]] for a more detailed explanation with examples as to how determining overlaps works.
 
= CigarRoller=
This class is part of [[C++ LibrarylibStatGen: libcsg|libcsggeneral]].
The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object. It is a child class of Cigar.
== Public Methods =={| style="marginSee: 1em 1em 1em 0; background-colorhttp: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"|-style="background: #f2f2f2; text-align: center;"! Method Name !! Description|-| <code>CigarRoller::CigarRoller()</code>| 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 += (const CigarOperator &rhs)</code>| Append the specified cigar operation to this object.|-| <code>CigarRoller & CigarRoller::operator = (CigarRoller &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 objectcsg.|-| <code>void CigarRoller::Add(const char *cigarString)</code>| Adds the specified cigarString to this objectsph.|-| <code>void CigarRoller::Add(CigarRoller &rhs)</code>| Adds the specified CIGAR to this objectumich.|-| <code>void CigarRoller::Set(const char *cigarString)<edu/code>| Sets this object to the specified cigarString.|-| <code>void CigarRoller::Set(const uint32_t* cigarBuffer, uint16_t bufferLen)</code>| Sets this object to the BAM formatted cigar found at the beginning of the specified buffer which is bufferLen long.|-| ''' DEPRECATED''' <code>int CigarRoller::getMatchPositionOffset()<mktrost/code>| DO NOT USE.|-| <code>const char * CigarRoller::getString()<doxygen/code>| Returns the string representation of this CIGAR object.|-| <code>void CigarRoller::clear()<current/code>| Clear this object so that it has 0 Cigar OperationsclassCigarRoller.|} == Overloaded Streaming Operators == {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"|-style="background: #f2f2f2; text-align: center;"! Method Name !! Description|-| <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 streamhtml for documentation.|} 
= Mapping Between Reference and Read/Query =
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