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= CigarRoller=
= Cigar=
This class is part of [[C++ Library: libcsg|libcsg]].
This class is part of [[C++ Library: libcsg|libcsg]].
This purpose of this class is to provide utilities for creating and processing CIGAR strings.
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.
== Public Methods ==
== Public Methods ==
! Method Name !! Description
! Method Name !! Description
|-
|-
| <code>CigarRoller::CigarRoller()</code>
| <code>Cigar::Cigar()</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>
| <code>void Cigar::getCigarString(String& cigarString)</code>
| Constructor that initializes the object with the specified cigarString.
| Sets the passed in String to the string representation of this CIGAR object.
|-
|-
| <code>void CigarRoller::Set(const char *cigarString)</code>
| <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")
| 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>
| <code>CigarOperator & CigarRoller::operator [] (int i)</code>
| Return the Cigar Operation at the specified index (starting at 0).
| Return the Cigar Operation at the specified index (starting at 0).
|-
|-
| <code>bool CigarRoller::operator == (CigarRoller &rhs)</code>
| <code>bool Cigar::operator == (CigarRoller &rhs)</code>
| Returns true if two Cigar Rollers are the same (the same operations of the same sizes)
| Returns true if two Cigars are the same (the same operations of the same sizes)
|-
|-
| <code>int CigarRoller::size()</code>
| <code>int Cigar::size()</code>
| Return the number of cigar operations in this object.
| Return the number of cigar operations in this object.
|-
|-
| <code>void CigarRoller::Dump()</code>
| <code>void Cigar::Dump()</code>
| Write this object as a string to cout.
| Write this object as a string to cout.
|-
|-
| <code>int CigarRoller::getExpectedQueryBaseCount()</code>
| <code>int Cigar::getExpectedQueryBaseCount()</code>
| Returns the expected read length
| Returns the expected read length
|-
|-
| <code>int CigarRoller::getExpectedReferenceBaseCount()</code>
| <code>int Cigar::getExpectedReferenceBaseCount()</code>
| Return how many bases in the reference are spanned by the given CIGAR string
| Return how many bases in the reference are spanned by the given CIGAR string
|-
|-
| <code>int32_t CigarRoller::getRefOffset(int32_t queryIndex)</code>
| <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.
|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.
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 CigarRoller::getQueryIndex(int32_t refOffset)</code>
| <code>int32_t Cigar::getQueryIndex(int32_t refOffset)</code>
| Return the query index associated with the specified reference offset or INDEX_NA based on this cigar.
| Return the query index associated with the specified reference offset 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.
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 CigarRoller::getRefPosition(int32_t queryIndex, int32_t queryStartPos)</code>
| <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.
|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.
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.
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 CigarRoller::getQueryIndex(int32_t refPosition, int32_t queryStartPos)</code>
| <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.
| 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.
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.
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 getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)</code>
| <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.
| 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.)
start : inclusive start position (reference position) of the region to check for overlaps in. (-1 indicates to start at the beginning of the reference.)
! Method Name !! Description
! Method Name !! Description
|-
|-
| <code> std::ostream &operator << (std::ostream &stream, const CigarRoller& roller)</code>
| <code> std::ostream &operator << (std::ostream &stream, const Cigar& cigar)</code>
| Writes all of the cigar operations contained in this roller to the passed in stream.
| Writes all of the cigar operations contained in the cigar to the passed in stream.
|-
|-
| <code> std::ostream &operator << (std::ostream &stream, const CigarRoller::CigarOperator& o)</code>
| <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).
| Writes the specified cigar operation to the specified stream as <count><char> (3M).
|}
|}
== Mapping Between Reference and Read/Query ==
= CigarRoller=
<code>int32_t CigarRoller::getRefOffset(int32_t queryIndex)</code> and <code>int32_t CigarRoller::getQueryIndex(int32_t refOffset)</code> are used to map between the reference and the read.
This class is part of [[C++ Library: libcsg|libcsg]].
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="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>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 += (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::Add(CigarRoller &rhs)</code>
| Adds the specified CIGAR to this object.
|-
| <code>void CigarRoller::Set(const char *cigarString)</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()</code>
| DO NOT USE.
|-
| <code>const char * CigarRoller::getString()</code>
| Returns the string representation of this CIGAR object.
|-
| <code>void CigarRoller::clear()</code>
| Clear this object so that it has 0 Cigar Operations.
|}
== 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 stream.
|}
= Mapping Between Reference and Read/Query =
<code>int32_t Cigar::getRefOffset(int32_t queryIndex)</code> and <code>int32_t Cigar::getQueryIndex(int32_t refOffset)</code> are used to map between the reference and the read.
The queryIndex is the index in the read - from 0 to (read length - 1).
The queryIndex is the index in the read - from 0 to (read length - 1).
== Determining the Number of Reference and Read/Query Overlaps ==
A useful concept is determining the number of bases that overlap between the reference and the read in a given region.
A useful concept is determining the number of bases that overlap between the reference and the read in a given region.
