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| CigarOperator (Operation operation, uint32_t count) |
| Set the cigar operator with the specified operation and count length. More...
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char | getChar () const |
| Get the character code (M, I, D, N, S, H, or P) associated with this operation. More...
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bool | operator== (const CigarOperator &rhs) const |
| Compare only on the operator, true if they are the same, false if not. Match and mismatch are considered the same for CIGAR strings. More...
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bool | operator!= (const CigarOperator &rhs) const |
| Compare only on the operator, false if they are the same, true if not. Match and mismatch are considered the same for CIGAR strings. More...
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Definition at line 107 of file Cigar.h.
◆ CigarOperator() [1/2]
Cigar::CigarOperator::CigarOperator |
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inline |
Definition at line 110 of file Cigar.h.
111 {
113 count = 0;
114 }
@ none
no operation has been set.
◆ CigarOperator() [2/2]
Cigar::CigarOperator::CigarOperator |
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Operation |
operation, |
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uint32_t |
count |
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) |
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inline |
Set the cigar operator with the specified operation and count length.
Definition at line 118 of file Cigar.h.
119 : operation(operation), count(count) {};
◆ getChar()
char Cigar::CigarOperator::getChar |
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const |
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inline |
Get the character code (M, I, D, N, S, H, or P) associated with this operation.
Definition at line 127 of file Cigar.h.
128 {
129 switch (operation)
130 {
132 return '?';
135 return'M';
137 return 'I';
139 return'D';
141 return 'N';
143 return 'S';
145 return 'H';
147 return 'P';
148 }
149 return '?';
150 }
@ del
deletion from the reference (the reference contains bases that have no corresponding base in the quer...
@ mismatch
mismatch operation. Associated with CIGAR Operation "M"
@ hardClip
Hard clip on the read (clipped sequence not present in the query sequence or reference)....
@ match
match/mismatch operation. Associated with CIGAR Operation "M"
@ pad
Padding (not in reference or query). Associated with CIGAR Operation "P".
@ insert
insertion to the reference (the query sequence contains bases that have no corresponding base in the ...
@ skip
skipped region from the reference (the reference contains bases that have no corresponding base in th...
@ softClip
Soft clip on the read (clipped sequence present in the query sequence, but not in reference)....
References Cigar::del, Cigar::hardClip, Cigar::insert, Cigar::match, Cigar::mismatch, Cigar::none, Cigar::pad, Cigar::skip, and Cigar::softClip.
◆ operator!=()
bool Cigar::CigarOperator::operator!= |
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const CigarOperator & |
rhs | ) |
const |
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inline |
Compare only on the operator, false if they are the same, true if not. Match and mismatch are considered the same for CIGAR strings.
Definition at line 163 of file Cigar.h.
164 {
165 return !((*this) == rhs) ;
166 }
◆ operator==()
bool Cigar::CigarOperator::operator== |
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const CigarOperator & |
rhs | ) |
const |
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inline |
Compare only on the operator, true if they are the same, false if not. Match and mismatch are considered the same for CIGAR strings.
Definition at line 153 of file Cigar.h.
154 {
155 if (operation==rhs.operation)
156 return true;
158 return true;
159 return false;
160 }
References Cigar::match, and Cigar::mismatch.
◆ count
uint32_t Cigar::CigarOperator::count |
◆ operation
The documentation for this struct was generated from the following file: