fhirtypes
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TypeScript
import { IBackboneElement, IElement } from '../base';
import { IReference } from '../datatypes';
/**
* @name IMolecularSequenceVariant
* @description Raw data describing a biological sequence.
* @see <a href="https://hl7.org/fhir/R4/molecularsequence-definitions.html#MolecularSequence.variant">IMolecularSequenceVariant</a>
* @version R4
* @extends {IBackboneElement}
* @author Claudia Alarcón Lazo
*/
export interface IMolecularSequenceVariant extends IBackboneElement {
/**
* @description Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
*/
start?: number;
/**
* @description Extensions for start
*/
_start?: IElement;
/**
* @description End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
*/
end?: number;
/**
* @description Extensions for end
*/
_end?: IElement;
/**
* @description An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
*/
observedAllele?: string;
/**
* @description Extensions for observedAllele
*/
_observedAllele?: IElement;
/**
* @description An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
*/
referenceAllele?: string;
/**
* @description Extensions for referenceAllele
*/
_referenceAllele?: IElement;
/**
* @description Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
*/
cigar?: string;
/**
* @description Extensions for cigar
*/
_cigar?: IElement;
/**
* @description A pointer to an Observation containing variant information.
*/
variantPointer?: IReference;
}