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| | + | [[Category:C++]] |
| | + | [[Category:libStatGen]] |
| | + | [[Category:libStatGen general]] |
| | + | |
| | = Cigar= | | = Cigar= |
| − | This class is part of [[C++ Library: libcsg|libcsg]]. | + | This class is part of [[libStatGen: general]]. |
| − | | |
| − | This 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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| − | | |
| − | == static Methods ==
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| − | These methods are helpful for determining information about the operator.
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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>bool foundInQuery(Operation op)</code>
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| − | | Return true if the specified operation is found in the query sequence, false if not.
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| − | |-
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| − | | <code>bool isClip(Operation op)</code>
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| − | | Return true if the specified operation is a clipping operation, false if not.
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| − | |-
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| − | |}
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| − | | |
| − | == Public Methods ==
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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>Cigar::Cigar()</code>
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| − | | Default constructor initializes as a CIGAR with no operations.
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| − | |-
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| − | | <code>void Cigar::getCigarString(String& cigarString)</code>
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| − | | Sets the passed in String to the string representation of this CIGAR object.
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| − | |-
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| − | | <code>void Cigar::getCigarString(std::string& cigarString)</code>
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| − | | Sets the passed in std::string to the string representation of this CIGAR object.
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| − | |-
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| − | | <code>void Cigar::getExpandedString(std::string &s)</code>
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| − | | Sets the specified string to a string of characters that represent this cigar with no digits (a CIGAR of "3M" would return "MMM")
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| − | |-
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| − | | <code>CigarOperator & Cigar::operator [] (int i)</code>
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| − | | Return the Cigar Operation at the specified index (starting at 0).
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| − | |-
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| − | | <code>bool Cigar::operator == (CigarRoller &rhs)</code>
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| − | | Returns true if two Cigars are the same (the same operations of the same sizes)
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| − | |-
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| − | | <code>int Cigar::size()</code>
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| − | | Return the number of cigar operations in this object.
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| − | |-
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| − | | <code>void Cigar::Dump()</code>
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| − | | Write this object as a string to cout.
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| − | |-
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| − | | <code>int Cigar::getExpectedQueryBaseCount()</code>
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| − | | Returns the expected read length
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| − | |-
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| − | | <code>int Cigar::getExpectedReferenceBaseCount()</code>
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| − | | Return how many bases in the reference are spanned by the given CIGAR string
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| − | |-
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| − | | <code>int Cigar::getNumBeginClips()</code>
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| − | | Return the number of clips that are at the beginning of the cigar.
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| − | |-
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| − | | <code>int Cigar::getNumEndClips()</code>
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| − | | Return the number of clips that are at the end of the cigar.
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| − | |-
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| − | | <code>int32_t Cigar::getRefOffset(int32_t queryIndex)</code>
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| − | |Return the reference offset associated with the specified query index or INDEX_NA based on this cigar.
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| − | See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how it works.
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| − | |-
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| − | | <code>int32_t Cigar::getQueryIndex(int32_t refOffset)</code>
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| − | | Return the query index associated with the specified reference offset or INDEX_NA based on this cigar.
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| − | See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how it works.
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| − | |-
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| − | | <code>int32_t Cigar::getRefPosition(int32_t queryIndex, int32_t queryStartPos)</code>
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| − | |Return the reference position associated with the specified query index or INDEX_NA based on this cigar and the specified queryStartPos.
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| − | queryStartPops is the leftmost mapping position of the first matching base in the query.
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| − | | |
| − | See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how it works.
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| − | |-
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| − | | <code>int32_t Cigar::getQueryIndex(int32_t refPosition, int32_t queryStartPos)</code>
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| − | | Return the query index associated with the specified reference position and queryStartPos or INDEX_NA based on this cigar.
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| − | queryStartPops is the leftmost mapping position of the first matching base in the query.
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| − | | |
| − | See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how it works.
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| − | |-
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| − | | <code>uint32_t Cigar::getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)</code>
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| − | | Return the number of bases that overlap the reference and the read associated with this cigar that falls within the specified region.
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| − | start : inclusive start position (reference position) of the region to check for overlaps in. (-1 indicates to start at the beginning of the reference.)
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| − |
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| − | end : exclusive end position (reference position) of the region to check for overlaps in. (-1 indicates to go to the end of the reference.)
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| − | | |
| − | queryStartPos : leftmost mapping position of the first matching base in the query.
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| − | | |
| − | NOTE: ensure that start, end, and queryStartPos are all in the same base (0 or 1).
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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 it works.
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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 Cigar& cigar)</code>
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| − | | Writes all of the cigar operations contained in the cigar to the passed in stream.
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| − | |-
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| − | | <code> std::ostream &operator << (std::ostream &stream, const Cigar::CigarOperator& o)</code>
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| − | | Writes the specified cigar operation to the specified stream as <count><char> (3M).
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| − | |}
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| − | | |
| − | | |
| − | | |
| − | == Public Enums ==
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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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| − | ! colspan="2"| enum SPACE_TYPE
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| − | |-
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| − | ! Enum Value !! Description
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| − | |-
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| − | | none
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| − | | No operation has been specified
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| − | |-
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| − | | match
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| − | | The query sequence and the reference sequence bases are the same for the bases associated with this cigar operation.
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| − | Both <code>match</code> and <code>mismatch</code> are associated with CIGAR Operation "M"
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| − | |-
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| − | | mismatch
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| − | | The query sequence and the reference sequence bases are different for the bases associated with this cigar operation, but bases exist in both the query and the reference.
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| − | Both <code>match</code> and <code>mismatch</code> are associated with CIGAR Operation "M"
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| − | |-
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| − | | insert
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| − | | Insertion to the reference (the query sequence contains bases that have no corresponding base in the reference).
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| − | Associated with CIGAR Operation "I"
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| − | |-
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| − | | del
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| − | |Deletion from the reference (the reference contains bases that have no corresponding base in the query sequence).
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| − | Associated with CIGAR Operation "D"
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| − | |-
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| − | | skip
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| − | | Skipped region from the reference (the reference contains bases that have no corresponding base in the query sequence).
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| − | Associated with CIGAR Operation "N"
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| − | |-
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| − | | softClip
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| − | | Soft clip on the read (clipped sequence present in the query sequence)
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| − | Associated with CIGAR Operation "S"
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| − | |-
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| − | | hardClip
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| − | | Hard clip on the read (clipped sequence not present in the query sequence)
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| − | Associated with CIGAR Operation "H"
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| − | |-
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| − | |pad
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| − | | Padding (silent deletion from the padded reference sequence)
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| − | Associated with CIGAR Operation "P"
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| − | |}
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| − | | |
| − | | |
| − | == Public Constants ==
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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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| − | ! Constant !! Value !! Description
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| − | |-
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| − | | INDEX_NA
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| − | | -1
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| − | | Value associated with an index that is not applicable/does not exist.
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| − | Used for converting between query and reference indexes/offsets when an associated index/offset does not exist.
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| − | |}
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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. |
| | | | |
| − | == Nested Class ==
| + | See: http://csg.sph.umich.edu//mktrost/doxygen/current/classCigar.html for documentation. |
| | | | |
| − | === CigarOperation ===
| + | The static methods are helpful for determining information about the operator. |
| | | | |
| − | ==== Public Methods ====
| + | See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how the mapping between the read/query works. |
| − | {| 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>CigarOperator::CigarOperator(Operation operation, uint32_t count)</code>
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| − | | Set the cigar operator with the specified operation and count length. | |
| − | |-
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| − | | <code>char CigarOperator::getChar()</code>
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| − | | Returns the character code (M, I, D, N, S, H, or P) associated with this operation.
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| − | |-
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| − | | <code>bool CigarOperator::operator == (CigarOperator &rhs)</code>
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| − | | Returns true if the passed in operator is the same as this operator, false if not.
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| − | |-
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| − | | <code>bool CigarOperator::operator != (CigarOperator &rhs)</code>
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| − | | Returns true if the passed in operator is not the same as this operator, false if they are the same.
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| − | |}
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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. |
| | | | |
| | = CigarRoller= | | = CigarRoller= |
| − | This class is part of [[C++ Library: libcsg|libcsg]]. | + | This class is part of [[libStatGen: general]]. |
| | | | |
| | 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. |
| | | | |
| − | == 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 += (CigarOperator &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 = |
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| | getNumOverlaps(0,5,1) = 4 - with a different start position, this range overlaps the read with 4 bases | | getNumOverlaps(0,5,1) = 4 - with a different start position, this range overlaps the read with 4 bases |
| | getNumOverlaps(32,40,32) = 4 - with a different start position, this range overlaps the read with 4 bases | | getNumOverlaps(32,40,32) = 4 - with a different start position, this range overlaps the read with 4 bases |
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| − |
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| − | [[Category:C++]]
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| − | [[Category:libcsg]]
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