cgatools::variants::Allele Class Reference
A class that corresponds to a single allele within a locus in a Complete Genomics variant file.
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#include <Allele.hpp>
List of all members.
Public Member Functions |
| | Allele () |
| | Construct the Allele.
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| | Allele (const Locus *locus) |
| | Construct the Allele.
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| const std::vector< size_t > & | getCallOffsets () const |
| | Returns the offsets of the calls for this Allele within locus_->getCalls().
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const Call & | getCall (size_t index) const |
| std::string | getAlleleSequence () const |
| | Returns the sequence of this Allele of this Locus, replacing "=" with the corresponding reference sequence.
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| std::string | getRefSequence () const |
| | Returns the reference sequence corresponding to this Locus, replacing "=" with the corresponding reference sequence.
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| const std::string & | getHapLink () const |
| | Returns the first hapLink specified for this Allele, in call order.
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uint32_t | getMinScore () const |
| | Returns the minimum score of all calls in this Allele.
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| bool | hasNoCalls () const |
| | Returns true iff this Allele has one or more calls whose sequence contains N or ? characters.
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void | clearCalls () |
| | Clears out the set of calls associated with this Allele.
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void | addCallOffset (size_t offset) |
| | Associates a call in locus_->getCalls() with this Allele.
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void | setLocus (const Locus *locus) |
| | Sets the locus for this Allele.
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Detailed Description
A class that corresponds to a single allele within a locus in a Complete Genomics variant file.
Constructor & Destructor Documentation
| cgatools::variants::Allele::Allele |
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[inline] |
Construct the Allele.
The Allele cannot be used until its locus is set and its call offsets are set.
| cgatools::variants::Allele::Allele |
( |
const Locus * |
locus |
) |
[inline] |
Construct the Allele.
The Allele cannot be used until its call offsets are set.
Member Function Documentation
| std::string cgatools::variants::Allele::getAlleleSequence |
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const |
Returns the sequence of this Allele of this Locus, replacing "=" with the corresponding reference sequence.
| const std::vector<size_t>& cgatools::variants::Allele::getCallOffsets |
( |
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) |
const [inline] |
Returns the offsets of the calls for this Allele within locus_->getCalls().
| const std::string& cgatools::variants::Allele::getHapLink |
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const |
Returns the first hapLink specified for this Allele, in call order.
| std::string cgatools::variants::Allele::getRefSequence |
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) |
const |
Returns the reference sequence corresponding to this Locus, replacing "=" with the corresponding reference sequence.
| bool cgatools::variants::Allele::hasNoCalls |
( |
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) |
const |
Returns true iff this Allele has one or more calls whose sequence contains N or ? characters.
The documentation for this class was generated from the following file:
1.6.2
