static MolecularSequence.Variant.Builder |
MolecularSequence.Variant.builder() |
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.cigar(String cigar) |
Extended CIGAR string for aligning the sequence with reference bases.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.cigar(String cigar) |
Convenience method for setting cigar .
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.end(Integer end) |
End position of the variant on the reference sequence.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.end(Integer end) |
Convenience method for setting end .
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.extension(Extension... extension) |
May be used to represent additional information that is not part of the basic definition of the element.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.extension(Collection<Extension> extension) |
May be used to represent additional information that is not part of the basic definition of the element.
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protected MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.from(MolecularSequence.Variant variant) |
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.id(String id) |
Unique id for the element within a resource (for internal references).
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.modifierExtension(Extension... modifierExtension) |
May be used to represent additional information that is not part of the basic definition of the element and that
modifies the understanding of the element in which it is contained and/or the understanding of the containing
element's descendants.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.modifierExtension(Collection<Extension> modifierExtension) |
May be used to represent additional information that is not part of the basic definition of the element and that
modifies the understanding of the element in which it is contained and/or the understanding of the containing
element's descendants.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.observedAllele(String observedAllele) |
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.observedAllele(String observedAllele) |
Convenience method for setting observedAllele .
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.referenceAllele(String referenceAllele) |
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.referenceAllele(String referenceAllele) |
Convenience method for setting referenceAllele .
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.start(Integer start) |
Start position of the variant on the reference sequence.
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.start(Integer start) |
Convenience method for setting start .
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.toBuilder() |
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MolecularSequence.Variant.Builder |
MolecularSequence.Variant.Builder.variantPointer(Reference variantPointer) |
A pointer to an Observation containing variant information.
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