Difference between revisions of "C++ Class: CigarRoller"
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| − | | | + | | Default constructor initializes as a CIGAR with no operations. |
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Revision as of 14:55, 13 May 2010
CigarRoller
This class is part of libcsg.
This purpose of this class is to provide utilities for creating and processing CIGAR strings.
Public Methods
| Method Name | Description |
|---|---|
CigarRoller::CigarRoller()
|
Default constructor initializes as a CIGAR with no operations. |
Overloaded Streaming Operators
| Method Name | Description |
|---|---|
std::ostream &operator << (std::ostream &stream, const CigarRoller& roller)
|
Writes all of the cigar operations contained in this roller to the passed in stream. |
Public Enums
| 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 |
| 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 |
| 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
| 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
| Method Name | Description |
|---|---|
CigarOperator::CigarOperator(Operation operation, uint32_t count)
|
Set the cigar operator with the specified operation and count length. |
char CigarOperator::getChar()
|
Returns the character code (M, I, D, N, S, H, or P) associated with this operation. |
bool CigarOperator::operator == (CigarOperator &rhs)
|
Returns true if the passed in operator is the same as this operator, false if not. |
bool CigarOperator::operator != (CigarOperator &rhs)
|
Returns true if the passed in operator is not the same as this operator, false if they are the same. |
