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C++ Class: CigarRoller

7,953 bytes removed, 18:05, 23 August 2011
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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.
== static Methods ==These methods are helpful See: [http://www.sph.umich.edu/csg/mktrost/doxygen/current/classCigar.html http://www.sph.umich.edu/csg/mktrost/doxygen/current/classCigar.html] for determining information about the operatordocumentation.
{| 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>bool Cigar::foundInQuery(Operation op)</code>| Return true if The static methods are helpful for determining information about the specified operation is found in the query sequence, false if not.|-| <code>bool Cigar::isClip(Operation op)</code>| Return true if the specified operation is a clipping operation, false if notoperator.|-|}
== Public Methods =={| 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>Cigar::Cigar()</code>| Default constructor initializes as a CIGAR with no operations.|-| <code>void Cigar::getCigarString(String& cigarString)</code>| Sets the passed in String to the string representation of this CIGAR object.|-| <code>void Cigar::getCigarString(std::string& cigarString)</code>| Sets the passed in std::string to the string representation of this CIGAR object.|-| <code>void Cigar::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>CigarOperator & Cigar::operator [] (int i)</code>| Return the Cigar Operation at the specified index (starting at 0).|-| <code>CigarOperator & Cigar::getOperator(int i)</code>| Return the Cigar Operation at the specified index (starting at 0).|-| <code>bool Cigar::operator == (CigarRoller &rhs)</code>| Returns true if two Cigars are the same (the same operations of the same sizes)|-| <code>int Cigar::size()</code>| Return the number of cigar operations in this object.|-| <code>void Cigar::Dump()</code>| Write this object as a string to cout.|-| <code>int Cigar::getExpectedQueryBaseCount()</code>| Returns the expected read length|-| <code>int Cigar::getExpectedReferenceBaseCount()</code>| Return how many bases in the reference are spanned by the given CIGAR string|-| <code>int Cigar::getNumBeginClips()</code>| Return the number of clips that are at the beginning of the cigar.|-| <code>int Cigar::getNumEndClips()</code>| Return the number of clips that are at the end of the cigar.|-| <code>int32_t Cigar::getRefOffset(int32_t queryIndex)</code>|Return the reference offset associated with the specified query index or INDEX_NA based on this cigar.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.|-| <code>int32_t Cigar::getQueryIndex(int32_t refOffset)</code>| Return the query index associated with mapping between the specified reference offset or INDEX_NA based on this cigar.See [[C++ Class: CigarRoller#Mapping Between Reference and Readread/Query|Mapping Between Reference and Read/Query]] for a more detailed explanation with examples as to how it query works.|-| <code>int32_t Cigar::getRefPosition(int32_t queryIndex, int32_t queryStartPos)</code>|Return the reference position associated with the specified query index or INDEX_NA based on this cigar and the specified queryStartPos. queryStartPops is the leftmost mapping position of the first matching base in the query.
See [[C++ Class: CigarRoller#Mapping Between Determining the Number of Reference and Read/QueryOverlaps|Mapping Between Determining the Number of Reference and Read/QueryOverlaps]] for a more detailed explanation with examples as to how it determining overlaps works.|-| <code>int32_t Cigar::getQueryIndex(int32_t refPosition, int32_t queryStartPos)</code>| Return the query index associated with the specified reference position and queryStartPos or INDEX_NA based on this cigar.queryStartPops is the leftmost mapping position of the first matching base in the query.
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.
|-
| <code>uint32_t Cigar::getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)</code>
| Return the number of bases that overlap the reference and the read associated with this cigar that falls within the specified region.
start : inclusive start position (reference position) of the region to check for overlaps in. (-1 indicates to start at the beginning of the reference.)
end : exclusive end position (reference position) of the region to check for overlaps in. (-1 indicates to go to the end of the reference.)
 
queryStartPos : leftmost mapping position of the first matching base in the query.
 
NOTE: ensure that start, end, and queryStartPos are all in the same base (0 or 1).
 
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.
 
|}
 
== 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 Cigar& cigar)</code>
| Writes all of the cigar operations contained in the cigar to the passed in stream.
|-
| <code> std::ostream &operator << (std::ostream &stream, const Cigar::CigarOperator& o)</code>
| Writes the specified cigar operation to the specified stream as <count><char> (3M).
|}
 
 
 
== Public Enums ==
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-style="background: #f2f2f2; text-align: center;"
! colspan="2"| enum SPACE_TYPE
|-
! Enum Value !! Description
|-
| none
| No operation has been specified
|-
| match
| The query sequence and the reference sequence bases are the same for the bases associated with this cigar operation.
Both <code>match</code> and <code>mismatch</code> are associated with CIGAR Operation "M"
|-
| mismatch
| 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.
Both <code>match</code> and <code>mismatch</code> are associated with CIGAR Operation "M"
|-
| insert
| Insertion to the reference (the query sequence contains bases that have no corresponding base in the reference).
Associated with CIGAR Operation "I"
|-
| del
|Deletion from the reference (the reference contains bases that have no corresponding base in the query sequence).
Associated with CIGAR Operation "D"
|-
| skip
| Skipped region from the reference (the reference contains bases that have no corresponding base in the query sequence).
Associated with CIGAR Operation "N"
|-
| softClip
| Soft clip on the read (clipped sequence present in the query sequence)
Associated with CIGAR Operation "S"
|-
| hardClip
| Hard clip on the read (clipped sequence not present in the query sequence)
Associated with CIGAR Operation "H"
|-
|pad
| Padding (silent deletion from the padded reference sequence)
Associated with CIGAR Operation "P"
|}
 
 
== Public Constants ==
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
|-style="background: #f2f2f2; text-align: center;"
! Constant !! Value !! Description
|-
| INDEX_NA
| -1
| Value associated with an index that is not applicable/does not exist.
Used for converting between query and reference indexes/offsets when an associated index/offset does not exist.
|}
 
 
== Nested Class ==
 
=== CigarOperation ===
 
==== Public Methods ====
{| 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>CigarOperator::CigarOperator(Operation operation, uint32_t count)</code>
| Set the cigar operator with the specified operation and count length.
|-
| <code>char CigarOperator::getChar()</code>
| Returns the character code (M, I, D, N, S, H, or P) associated with this operation.
|-
| <code>bool CigarOperator::operator == (const CigarOperator &rhs)</code>
| Returns true if the passed in operator is the same as this operator, false if not.
|-
| <code>bool CigarOperator::operator != (const CigarOperator &rhs)</code>
| Returns true if the passed in operator is not the same as this operator, false if they are the same.
|}
= CigarRoller=

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