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= CigarRoller=
This class is part of [[C++ Library: libcsg|libcsg]].
This purpose of this class is to provide utilities for creating and processing CIGAR strings.
== 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
|-
| void BaseAsciiMap::setBaseMapType(SPACE_TYPE spaceType)
| Set the base type based on the passed in option.
|}
== 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.
|}
== 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 == (CigarOperator &rhs)</code>
| Returns true if the passed in operator is the same as this operator, false if not.
|-
| <code>bool CigarOperator::operator != (CigarOperator &rhs)</code>
| Returns true if the passed in operator is not the same as this operator, false if they are the same.
|}
This class is part of [[C++ Library: libcsg|libcsg]].
This purpose of this class is to provide utilities for creating and processing CIGAR strings.
== 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
|-
| void BaseAsciiMap::setBaseMapType(SPACE_TYPE spaceType)
| Set the base type based on the passed in option.
|}
== 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.
|}
== 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 == (CigarOperator &rhs)</code>
| Returns true if the passed in operator is the same as this operator, false if not.
|-
| <code>bool CigarOperator::operator != (CigarOperator &rhs)</code>
| Returns true if the passed in operator is not the same as this operator, false if they are the same.
|}
