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| | = Cigar= | | = Cigar= |
| − | This class is part of [[C++ Library: libStatGen]]. | + | This class is part of [[libStatGen: general]]. |
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| | 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. | | 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. |
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| − | 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. | + | See: http://csg.sph.umich.edu//mktrost/doxygen/current/classCigar.html for documentation. |
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| | The static methods are helpful for determining information about the operator. | | The static methods are helpful for determining information about the operator. |
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| | 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. | | 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. |
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| | = CigarRoller= | | = CigarRoller= |
| − | This class is part of [[C++ Library: libcsg|libcsg]]. | + | This class is part of [[libStatGen: general]]. |
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| | The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object. It is a child class of Cigar. | | The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object. It is a child class of Cigar. |
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| − | == Public Methods ==
| + | See: http://csg.sph.umich.edu//mktrost/doxygen/current/classCigarRoller.html for documentation. |
| − | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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| − | |-style="background: #f2f2f2; text-align: center;"
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| − | ! Method Name !! Description
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| − | |-
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| − | | <code>CigarRoller::CigarRoller()</code>
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| − | | Default constructor initializes as a CIGAR with no operations.
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| − | |-
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| − | | <code>CigarRoller::CigarRoller(const char *cigarString)</code>
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| − | | Constructor that initializes the object with the specified cigarString.
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| − | |-
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| − | | <code>CigarRoller & CigarRoller::operator += (CigarRoller &rhs)</code>
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| − | | Add the contents of the specified CigarRoller to this object.
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| − | |-
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| − | | <code>CigarRoller & CigarRoller::operator += (const CigarOperator &rhs)</code>
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| − | | Append the specified cigar operation to this object.
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| − | |-
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| − | | <code>CigarRoller & CigarRoller::operator = (CigarRoller &rhs)</code>
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| − | | Append the specified cigar operation to this object.
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| − | |-
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| − | | <code>void CigarRoller::Add(Operation operation, int count)</code>
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| − | | Adds the specified operation with the specified count to this object.
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| − | |-
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| − | | <code>void CigarRoller::Add(const char *cigarString)</code>
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| − | | Adds the specified cigarString to this object.
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| − | |-
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| − | | <code>void CigarRoller::Add(CigarRoller &rhs)</code>
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| − | | Adds the specified CIGAR to this object.
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| − | |-
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| − | | <code>void CigarRoller::Set(const char *cigarString)</code>
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| − | | Sets this object to the specified cigarString.
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| − | |-
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| − | | <code>void CigarRoller::Set(const uint32_t* cigarBuffer, uint16_t bufferLen)</code>
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| − | | Sets this object to the BAM formatted cigar found at the beginning of the specified buffer which is bufferLen long.
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| − | |-
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| − | | ''' DEPRECATED''' <code>int CigarRoller::getMatchPositionOffset()</code>
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| − | | DO NOT USE.
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| − | |-
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| − | | <code>const char * CigarRoller::getString()</code>
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| − | | Returns the string representation of this CIGAR object.
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| − | |-
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| − | | <code>void CigarRoller::clear()</code>
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| − | | Clear this object so that it has 0 Cigar Operations.
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| − | |}
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| − | | |
| − | == Overloaded Streaming Operators ==
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| − | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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| − | |-style="background: #f2f2f2; text-align: center;"
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| − | ! Method Name !! Description
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| − | |-
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| − | | <code> std::ostream &operator << (std::ostream &stream, const CigarRoller& roller)</code>
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| − | | Writes all of the cigar operations contained in this roller to the passed in stream.
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| − | |}
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| − | | |
| | | | |
| | = Mapping Between Reference and Read/Query = | | = Mapping Between Reference and Read/Query = |
