@medplum/core 0.1.6 → 0.3.0

package/dist/fhir/MolecularSequence.d.ts

@@ -1,746 +0,0 @@
-import { CodeableConcept } from './CodeableConcept';
-import { Extension } from './Extension';
-import { Identifier } from './Identifier';
-import { Meta } from './Meta';
-import { Narrative } from './Narrative';
-import { Quantity } from './Quantity';
-import { Reference } from './Reference';
-import { Resource } from './Resource';
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequence {
-    /**
-     * This is a MolecularSequence resource
-     */
-    readonly resourceType: 'MolecularSequence';
-    /**
-     * The logical id of the resource, as used in the URL for the resource.
-     * Once assigned, this value never changes.
-     */
-    readonly id?: string;
-    /**
-     * The metadata about the resource. This is content that is maintained by
-     * the infrastructure. Changes to the content might not always be
-     * associated with version changes to the resource.
-     */
-    readonly meta?: Meta;
-    /**
-     * A reference to a set of rules that were followed when the resource was
-     * constructed, and which must be understood when processing the content.
-     * Often, this is a reference to an implementation guide that defines the
-     * special rules along with other profiles etc.
-     */
-    readonly implicitRules?: string;
-    /**
-     * The base language in which the resource is written.
-     */
-    readonly language?: string;
-    /**
-     * A human-readable narrative that contains a summary of the resource and
-     * can be used to represent the content of the resource to a human. The
-     * narrative need not encode all the structured data, but is required to
-     * contain sufficient detail to make it "clinically safe" for a human to
-     * just read the narrative. Resource definitions may define what content
-     * should be represented in the narrative to ensure clinical safety.
-     */
-    readonly text?: Narrative;
-    /**
-     * These resources do not have an independent existence apart from the
-     * resource that contains them - they cannot be identified independently,
-     * and nor can they have their own independent transaction scope.
-     */
-    readonly contained?: Resource[];
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the resource. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the resource and that modifies the
-     * understanding of the element that contains it and/or the understanding
-     * of the containing element's descendants. Usually modifier elements
-     * provide negation or qualification. To make the use of extensions safe
-     * and manageable, there is a strict set of governance applied to the
-     * definition and use of extensions. Though any implementer is allowed to
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension. Applications processing a
-     * resource are required to check for modifier extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * A unique identifier for this particular sequence instance. This is a
-     * FHIR-defined id.
-     */
-    readonly identifier?: Identifier[];
-    /**
-     * Amino Acid Sequence/ DNA Sequence / RNA Sequence.
-     */
-    readonly type?: string;
-    /**
-     * Whether the sequence is numbered starting at 0 (0-based numbering or
-     * coordinates, inclusive start, exclusive end) or starting at 1 (1-based
-     * numbering, inclusive start and inclusive end).
-     */
-    readonly coordinateSystem?: number;
-    /**
-     * The patient whose sequencing results are described by this resource.
-     */
-    readonly patient?: Reference;
-    /**
-     * Specimen used for sequencing.
-     */
-    readonly specimen?: Reference;
-    /**
-     * The method for sequencing, for example, chip information.
-     */
-    readonly device?: Reference;
-    /**
-     * The organization or lab that should be responsible for this result.
-     */
-    readonly performer?: Reference;
-    /**
-     * The number of copies of the sequence of interest. (RNASeq).
-     */
-    readonly quantity?: Quantity;
-    /**
-     * A sequence that is used as a reference to describe variants that are
-     * present in a sequence analyzed.
-     */
-    readonly referenceSeq?: MolecularSequenceReferenceSeq;
-    /**
-     * The definition of variant here originates from Sequence ontology
-     * ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)).
-     * This element can represent amino acid or nucleic sequence
-     * change(including insertion,deletion,SNP,etc.)  It can represent some
-     * complex mutation or segment variation with the assist of CIGAR string.
-     */
-    readonly variant?: MolecularSequenceVariant[];
-    /**
-     * Sequence that was observed. It is the result marked by referenceSeq
-     * along with variant records on referenceSeq. This shall start from
-     * referenceSeq.windowStart and end by referenceSeq.windowEnd.
-     */
-    readonly observedSeq?: string;
-    /**
-     * An experimental feature attribute that defines the quality of the
-     * feature in a quantitative way, such as a phred quality score
-     * ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
-     */
-    readonly quality?: MolecularSequenceQuality[];
-    /**
-     * Coverage (read depth or depth) is the average number of reads
-     * representing a given nucleotide in the reconstructed sequence.
-     */
-    readonly readCoverage?: number;
-    /**
-     * Configurations of the external repository. The repository shall store
-     * target's observedSeq or records related with target's observedSeq.
-     */
-    readonly repository?: MolecularSequenceRepository[];
-    /**
-     * Pointer to next atomic sequence which at most contains one variant.
-     */
-    readonly pointer?: Reference[];
-    /**
-     * Information about chromosome structure variation.
-     */
-    readonly structureVariant?: MolecularSequenceStructureVariant[];
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceInner {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * Structural variant inner start. If the coordinate system is either
-     * 0-based or 1-based, then start position is inclusive.
-     */
-    readonly start?: number;
-    /**
-     * Structural variant inner end. 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.
-     */
-    readonly end?: number;
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceOuter {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * Structural variant outer start. If the coordinate system is either
-     * 0-based or 1-based, then start position is inclusive.
-     */
-    readonly start?: number;
-    /**
-     * Structural variant outer end. 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.
-     */
-    readonly end?: number;
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceQuality {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * INDEL / SNP / Undefined variant.
-     */
-    readonly type?: string;
-    /**
-     * Gold standard sequence used for comparing against.
-     */
-    readonly standardSequence?: CodeableConcept;
-    /**
-     * Start position of the sequence. If the coordinate system is either
-     * 0-based or 1-based, then start position is inclusive.
-     */
-    readonly start?: number;
-    /**
-     * End position of the 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.
-     */
-    readonly end?: number;
-    /**
-     * The score of an experimentally derived feature such as a p-value
-     * ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
-     */
-    readonly score?: Quantity;
-    /**
-     * Which method is used to get sequence quality.
-     */
-    readonly method?: CodeableConcept;
-    /**
-     * True positives, from the perspective of the truth data, i.e. the
-     * number of sites in the Truth Call Set for which there are paths
-     * through the Query Call Set that are consistent with all of the alleles
-     * at this site, and for which there is an accurate genotype call for the
-     * event.
-     */
-    readonly truthTP?: number;
-    /**
-     * True positives, from the perspective of the query data, i.e. the
-     * number of sites in the Query Call Set for which there are paths
-     * through the Truth Call Set that are consistent with all of the alleles
-     * at this site, and for which there is an accurate genotype call for the
-     * event.
-     */
-    readonly queryTP?: number;
-    /**
-     * False negatives, i.e. the number of sites in the Truth Call Set for
-     * which there is no path through the Query Call Set that is consistent
-     * with all of the alleles at this site, or sites for which there is an
-     * inaccurate genotype call for the event. Sites with correct variant but
-     * incorrect genotype are counted here.
-     */
-    readonly truthFN?: number;
-    /**
-     * False positives, i.e. the number of sites in the Query Call Set for
-     * which there is no path through the Truth Call Set that is consistent
-     * with this site. Sites with correct variant but incorrect genotype are
-     * counted here.
-     */
-    readonly queryFP?: number;
-    /**
-     * The number of false positives where the non-REF alleles in the Truth
-     * and Query Call Sets match (i.e. cases where the truth is 1/1 and the
-     * query is 0/1 or similar).
-     */
-    readonly gtFP?: number;
-    /**
-     * QUERY.TP / (QUERY.TP + QUERY.FP).
-     */
-    readonly precision?: number;
-    /**
-     * TRUTH.TP / (TRUTH.TP + TRUTH.FN).
-     */
-    readonly recall?: number;
-    /**
-     * Harmonic mean of Recall and Precision, computed as: 2 * precision *
-     * recall / (precision + recall).
-     */
-    readonly fScore?: number;
-    /**
-     * Receiver Operator Characteristic (ROC) Curve  to give
-     * sensitivity/specificity tradeoff.
-     */
-    readonly roc?: MolecularSequenceRoc;
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceReferenceSeq {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * Structural unit composed of a nucleic acid molecule which controls its
-     * own replication through the interaction of specific proteins at one or
-     * more origins of replication
-     * ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).
-     */
-    readonly chromosome?: CodeableConcept;
-    /**
-     * The Genome Build used for reference, following GRCh build versions
-     * e.g. 'GRCh 37'.  Version number must be included if a versioned
-     * release of a primary build was used.
-     */
-    readonly genomeBuild?: string;
-    /**
-     * A relative reference to a DNA strand based on gene orientation. The
-     * strand that contains the open reading frame of the gene is the "sense"
-     * strand, and the opposite complementary strand is the "antisense"
-     * strand.
-     */
-    readonly orientation?: string;
-    /**
-     * Reference identifier of reference sequence submitted to NCBI. It must
-     * match the type in the MolecularSequence.type field. For example, the
-     * prefix, “NG_” identifies reference sequence for genes, “NM_” for
-     * messenger RNA transcripts, and “NP_” for amino acid sequences.
-     */
-    readonly referenceSeqId?: CodeableConcept;
-    /**
-     * A pointer to another MolecularSequence entity as reference sequence.
-     */
-    readonly referenceSeqPointer?: Reference;
-    /**
-     * A string like "ACGT".
-     */
-    readonly referenceSeqString?: string;
-    /**
-     * An absolute reference to a strand. The Watson strand is the strand
-     * whose 5'-end is on the short arm of the chromosome, and the Crick
-     * strand as the one whose 5'-end is on the long arm.
-     */
-    readonly strand?: string;
-    /**
-     * Start position of the window on the reference sequence. If the
-     * coordinate system is either 0-based or 1-based, then start position is
-     * inclusive.
-     */
-    readonly windowStart?: number;
-    /**
-     * End position of the window 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.
-     */
-    readonly windowEnd?: number;
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceRepository {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * Click and see / RESTful API / Need login to see / RESTful API with
-     * authentication / Other ways to see resource.
-     */
-    readonly type?: string;
-    /**
-     * URI of an external repository which contains further details about the
-     * genetics data.
-     */
-    readonly url?: string;
-    /**
-     * URI of an external repository which contains further details about the
-     * genetics data.
-     */
-    readonly name?: string;
-    /**
-     * Id of the variant in this external repository. The server will
-     * understand how to use this id to call for more info about datasets in
-     * external repository.
-     */
-    readonly datasetId?: string;
-    /**
-     * Id of the variantset in this external repository. The server will
-     * understand how to use this id to call for more info about variantsets
-     * in external repository.
-     */
-    readonly variantsetId?: string;
-    /**
-     * Id of the read in this external repository.
-     */
-    readonly readsetId?: string;
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceRoc {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * Invidual data point representing the GQ (genotype quality) score
-     * threshold.
-     */
-    readonly score?: number[];
-    /**
-     * The number of true positives if the GQ score threshold was set to
-     * "score" field value.
-     */
-    readonly numTP?: number[];
-    /**
-     * The number of false positives if the GQ score threshold was set to
-     * "score" field value.
-     */
-    readonly numFP?: number[];
-    /**
-     * The number of false negatives if the GQ score threshold was set to
-     * "score" field value.
-     */
-    readonly numFN?: number[];
-    /**
-     * Calculated precision if the GQ score threshold was set to "score"
-     * field value.
-     */
-    readonly precision?: number[];
-    /**
-     * Calculated sensitivity if the GQ score threshold was set to "score"
-     * field value.
-     */
-    readonly sensitivity?: number[];
-    /**
-     * Calculated fScore if the GQ score threshold was set to "score" field
-     * value.
-     */
-    readonly fMeasure?: number[];
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceStructureVariant {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * Information about chromosome structure variation DNA change type.
-     */
-    readonly variantType?: CodeableConcept;
-    /**
-     * Used to indicate if the outer and inner start-end values have the same
-     * meaning.
-     */
-    readonly exact?: boolean;
-    /**
-     * Length of the variant chromosome.
-     */
-    readonly length?: number;
-    /**
-     * Structural variant outer.
-     */
-    readonly outer?: MolecularSequenceOuter;
-    /**
-     * Structural variant inner.
-     */
-    readonly inner?: MolecularSequenceInner;
-}
-/**
- * Raw data describing a biological sequence.
- */
-export interface MolecularSequenceVariant {
-    /**
-     * Unique id for the element within a resource (for internal references).
-     * This may be any string value that does not contain spaces.
-     */
-    readonly id?: string;
-    /**
-     * May be used to represent additional information that is not part of
-     * the basic definition of the element. To make the use of extensions
-     * safe and manageable, there is a strict set of governance  applied to
-     * the definition and use of extensions. Though any implementer can
-     * define an extension, there is a set of requirements that SHALL be met
-     * as part of the definition of the extension.
-     */
-    readonly extension?: Extension[];
-    /**
-     * 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. Usually
-     * modifier elements provide negation or qualification. To make the use
-     * of extensions safe and manageable, there is a strict set of governance
-     * applied to the definition and use of extensions. Though any
-     * implementer can define an extension, there is a set of requirements
-     * that SHALL be met as part of the definition of the extension.
-     * Applications processing a resource are required to check for modifier
-     * extensions.
-     *
-     * Modifier extensions SHALL NOT change the meaning of any elements on
-     * Resource or DomainResource (including cannot change the meaning of
-     * modifierExtension itself).
-     */
-    readonly modifierExtension?: Extension[];
-    /**
-     * 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.
-     */
-    readonly start?: number;
-    /**
-     * 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.
-     */
-    readonly end?: number;
-    /**
-     * 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.
-     */
-    readonly observedAllele?: string;
-    /**
-     * 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.
-     */
-    readonly referenceAllele?: string;
-    /**
-     * 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).
-     */
-    readonly cigar?: string;
-    /**
-     * A pointer to an Observation containing variant information.
-     */
-    readonly variantPointer?: Reference;
-}