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3920 lines
189 KiB
TypeScript
3920 lines
189 KiB
TypeScript
// Type definitions for non-npm package Google Genomics API v1 1.0
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// Project: https://cloud.google.com/genomics
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// Definitions by: Bolisov Alexey <https://github.com/Bolisov>
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// Definitions: https://github.com/DefinitelyTyped/DefinitelyTyped
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// TypeScript Version: 2.3
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// IMPORTANT
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// This file was generated by https://github.com/Bolisov/google-api-typings-generator. Please do not edit it manually.
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// In case of any problems please post issue to https://github.com/Bolisov/google-api-typings-generator
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// Generated from: https://genomics.googleapis.com/$discovery/rest?version=v1
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/// <reference types="gapi.client" />
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declare namespace gapi.client {
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/** Load Genomics API v1 */
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function load(name: "genomics", version: "v1"): PromiseLike<void>;
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function load(name: "genomics", version: "v1", callback: () => any): void;
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const annotations: genomics.AnnotationsResource;
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const annotationsets: genomics.AnnotationsetsResource;
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const callsets: genomics.CallsetsResource;
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const datasets: genomics.DatasetsResource;
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const operations: genomics.OperationsResource;
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const readgroupsets: genomics.ReadgroupsetsResource;
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const reads: genomics.ReadsResource;
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const references: genomics.ReferencesResource;
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const referencesets: genomics.ReferencesetsResource;
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const variants: genomics.VariantsResource;
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const variantsets: genomics.VariantsetsResource;
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namespace genomics {
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interface Annotation {
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/** The annotation set to which this annotation belongs. */
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annotationSetId?: string;
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/** The end position of the range on the reference, 0-based exclusive. */
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end?: string;
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/** The server-generated annotation ID, unique across all annotations. */
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id?: string;
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/**
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* A map of additional read alignment information. This must be of the form
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* map<string, string[]> (string key mapping to a list of string values).
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*/
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info?: Record<string, any[]>;
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/** The display name of this annotation. */
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name?: string;
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/** The ID of the Google Genomics reference associated with this range. */
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referenceId?: string;
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/**
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* The display name corresponding to the reference specified by
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* `referenceId`, for example `chr1`, `1`, or `chrX`.
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*/
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referenceName?: string;
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/**
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* Whether this range refers to the reverse strand, as opposed to the forward
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* strand. Note that regardless of this field, the start/end position of the
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* range always refer to the forward strand.
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*/
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reverseStrand?: boolean;
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/** The start position of the range on the reference, 0-based inclusive. */
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start?: string;
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/**
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* A transcript value represents the assertion that a particular region of
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* the reference genome may be transcribed as RNA. An alternative splicing
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* pattern would be represented as a separate transcript object. This field
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* is only set for annotations of type `TRANSCRIPT`.
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*/
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transcript?: Transcript;
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/**
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* The data type for this annotation. Must match the containing annotation
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* set's type.
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*/
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type?: string;
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/**
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* A variant annotation, which describes the effect of a variant on the
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* genome, the coding sequence, and/or higher level consequences at the
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* organism level e.g. pathogenicity. This field is only set for annotations
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* of type `VARIANT`.
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*/
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variant?: VariantAnnotation;
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}
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interface AnnotationSet {
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/** The dataset to which this annotation set belongs. */
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datasetId?: string;
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/** The server-generated annotation set ID, unique across all annotation sets. */
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id?: string;
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/**
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* A map of additional read alignment information. This must be of the form
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* map<string, string[]> (string key mapping to a list of string values).
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*/
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info?: Record<string, any[]>;
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/** The display name for this annotation set. */
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name?: string;
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/**
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* The ID of the reference set that defines the coordinate space for this
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* set's annotations.
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*/
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referenceSetId?: string;
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/**
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* The source URI describing the file from which this annotation set was
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* generated, if any.
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*/
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sourceUri?: string;
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/** The type of annotations contained within this set. */
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type?: string;
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}
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interface BatchCreateAnnotationsRequest {
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/**
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* The annotations to be created. At most 4096 can be specified in a single
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* request.
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*/
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annotations?: Annotation[];
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/**
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* A unique request ID which enables the server to detect duplicated requests.
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* If provided, duplicated requests will result in the same response; if not
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* provided, duplicated requests may result in duplicated data. For a given
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* annotation set, callers should not reuse `request_id`s when writing
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* different batches of annotations - behavior in this case is undefined.
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* A common approach is to use a UUID. For batch jobs where worker crashes are
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* a possibility, consider using some unique variant of a worker or run ID.
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*/
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requestId?: string;
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}
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interface BatchCreateAnnotationsResponse {
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/**
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* The resulting per-annotation entries, ordered consistently with the
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* original request.
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*/
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entries?: Entry[];
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}
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interface Binding {
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/**
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* Specifies the identities requesting access for a Cloud Platform resource.
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* `members` can have the following values:
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*
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* * `allUsers`: A special identifier that represents anyone who is
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* on the internet; with or without a Google account.
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*
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* * `allAuthenticatedUsers`: A special identifier that represents anyone
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* who is authenticated with a Google account or a service account.
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*
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* * `user:{emailid}`: An email address that represents a specific Google
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* account. For example, `alice@gmail.com` or `joe@example.com`.
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*
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*
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* * `serviceAccount:{emailid}`: An email address that represents a service
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* account. For example, `my-other-app@appspot.gserviceaccount.com`.
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*
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* * `group:{emailid}`: An email address that represents a Google group.
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* For example, `admins@example.com`.
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*
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*
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* * `domain:{domain}`: A Google Apps domain name that represents all the
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* users of that domain. For example, `google.com` or `example.com`.
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*/
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members?: string[];
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/**
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* Role that is assigned to `members`.
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* For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
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* Required
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*/
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role?: string;
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}
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interface CallSet {
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/** The date this call set was created in milliseconds from the epoch. */
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created?: string;
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/** The server-generated call set ID, unique across all call sets. */
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id?: string;
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/**
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* A map of additional call set information. This must be of the form
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* map<string, string[]> (string key mapping to a list of string values).
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*/
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info?: Record<string, any[]>;
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/** The call set name. */
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name?: string;
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/** The sample ID this call set corresponds to. */
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sampleId?: string;
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/**
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* The IDs of the variant sets this call set belongs to. This field must
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* have exactly length one, as a call set belongs to a single variant set.
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* This field is repeated for compatibility with the
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* [GA4GH 0.5.1
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* API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76).
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*/
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variantSetIds?: string[];
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}
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interface CigarUnit {
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operation?: string;
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/** The number of genomic bases that the operation runs for. Required. */
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operationLength?: string;
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/**
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* `referenceSequence` is only used at mismatches
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* (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
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* Filling this field replaces SAM's MD tag. If the relevant information is
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* not available, this field is unset.
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*/
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referenceSequence?: string;
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}
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interface ClinicalCondition {
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/**
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* The MedGen concept id associated with this gene.
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* Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
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*/
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conceptId?: string;
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/** The set of external IDs for this condition. */
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externalIds?: ExternalId[];
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/** A set of names for the condition. */
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names?: string[];
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/**
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* The OMIM id for this condition.
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* Search for these IDs at http://omim.org/
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*/
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omimId?: string;
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}
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interface CodingSequence {
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/**
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* The end of the coding sequence on this annotation's reference sequence,
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* 0-based exclusive. Note that this position is relative to the reference
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* start, and *not* the containing annotation start.
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*/
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end?: string;
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/**
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* The start of the coding sequence on this annotation's reference sequence,
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* 0-based inclusive. Note that this position is relative to the reference
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* start, and *not* the containing annotation start.
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*/
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start?: string;
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}
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interface ComputeEngine {
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/** The names of the disks that were created for this pipeline. */
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diskNames?: string[];
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/** The instance on which the operation is running. */
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instanceName?: string;
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/** The machine type of the instance. */
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machineType?: string;
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/** The availability zone in which the instance resides. */
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zone?: string;
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}
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interface CoverageBucket {
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/**
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* The average number of reads which are aligned to each individual
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* reference base in this bucket.
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*/
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meanCoverage?: number;
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/** The genomic coordinate range spanned by this bucket. */
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range?: Range;
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}
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interface Dataset {
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/** The time this dataset was created, in seconds from the epoch. */
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createTime?: string;
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/** The server-generated dataset ID, unique across all datasets. */
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id?: string;
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/** The dataset name. */
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name?: string;
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/** The Google Cloud project ID that this dataset belongs to. */
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projectId?: string;
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}
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interface Entry {
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/** The created annotation, if creation was successful. */
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annotation?: Annotation;
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/** The creation status. */
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status?: Status;
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}
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interface Exon {
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/**
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* The end position of the exon on this annotation's reference sequence,
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* 0-based exclusive. Note that this is relative to the reference start, and
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* *not* the containing annotation start.
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*/
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end?: string;
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/**
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* The frame of this exon. Contains a value of 0, 1, or 2, which indicates
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* the offset of the first coding base of the exon within the reading frame
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* of the coding DNA sequence, if any. This field is dependent on the
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* strandedness of this annotation (see
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* Annotation.reverse_strand).
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* For forward stranded annotations, this offset is relative to the
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* exon.start. For reverse
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* strand annotations, this offset is relative to the
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* exon.end `- 1`.
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*
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* Unset if this exon does not intersect the coding sequence. Upon creation
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* of a transcript, the frame must be populated for all or none of the
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* coding exons.
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*/
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frame?: number;
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/**
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* The start position of the exon on this annotation's reference sequence,
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* 0-based inclusive. Note that this is relative to the reference start, and
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* **not** the containing annotation start.
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*/
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start?: string;
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}
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interface Experiment {
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/**
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* The instrument model used as part of this experiment. This maps to
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* sequencing technology in the SAM spec.
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*/
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instrumentModel?: string;
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/**
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* A client-supplied library identifier; a library is a collection of DNA
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* fragments which have been prepared for sequencing from a sample. This
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* field is important for quality control as error or bias can be introduced
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* during sample preparation.
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*/
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libraryId?: string;
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/**
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* The platform unit used as part of this experiment, for example
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* flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
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* @RG PU field in the SAM spec.
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*/
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platformUnit?: string;
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/** The sequencing center used as part of this experiment. */
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sequencingCenter?: string;
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}
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interface ExportReadGroupSetRequest {
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/**
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* Required. A Google Cloud Storage URI for the exported BAM file.
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* The currently authenticated user must have write access to the new file.
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* An error will be returned if the URI already contains data.
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*/
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exportUri?: string;
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/**
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* Required. The Google Cloud project ID that owns this
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* export. The caller must have WRITE access to this project.
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*/
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projectId?: string;
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/**
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* The reference names to export. If this is not specified, all reference
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* sequences, including unmapped reads, are exported.
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* Use `*` to export only unmapped reads.
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*/
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referenceNames?: string[];
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}
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interface ExportVariantSetRequest {
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/**
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* Required. The BigQuery dataset to export data to. This dataset must already
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* exist. Note that this is distinct from the Genomics concept of "dataset".
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*/
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bigqueryDataset?: string;
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/**
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* Required. The BigQuery table to export data to.
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* If the table doesn't exist, it will be created. If it already exists, it
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* will be overwritten.
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*/
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bigqueryTable?: string;
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/**
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* If provided, only variant call information from the specified call sets
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* will be exported. By default all variant calls are exported.
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*/
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callSetIds?: string[];
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/** The format for the exported data. */
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format?: string;
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/**
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* Required. The Google Cloud project ID that owns the destination
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* BigQuery dataset. The caller must have WRITE access to this project. This
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* project will also own the resulting export job.
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*/
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projectId?: string;
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}
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interface ExternalId {
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/** The id used by the source of this data. */
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id?: string;
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/** The name of the source of this data. */
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sourceName?: string;
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}
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interface ImportReadGroupSetsRequest {
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/**
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* Required. The ID of the dataset these read group sets will belong to. The
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* caller must have WRITE permissions to this dataset.
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*/
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datasetId?: string;
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/**
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* The partition strategy describes how read groups are partitioned into read
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* group sets.
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*/
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partitionStrategy?: string;
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/**
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* The reference set to which the imported read group sets are aligned to, if
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* any. The reference names of this reference set must be a superset of those
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* found in the imported file headers. If no reference set id is provided, a
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* best effort is made to associate with a matching reference set.
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*/
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referenceSetId?: string;
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/**
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* A list of URIs pointing at [BAM
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* files](https://samtools.github.io/hts-specs/SAMv1.pdf)
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* in Google Cloud Storage.
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* Those URIs can include wildcards (*), but do not add or remove
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* matching files before import has completed.
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*
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* Note that Google Cloud Storage object listing is only eventually
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* consistent: files added may be not be immediately visible to
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* everyone. Thus, if using a wildcard it is preferable not to start
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* the import immediately after the files are created.
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*/
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sourceUris?: string[];
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}
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interface ImportReadGroupSetsResponse {
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/** IDs of the read group sets that were created. */
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readGroupSetIds?: string[];
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}
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interface ImportVariantsRequest {
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/**
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* The format of the variant data being imported. If unspecified, defaults to
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* to `VCF`.
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*/
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format?: string;
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/**
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* A mapping between info field keys and the InfoMergeOperations to
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* be performed on them. This is plumbed down to the MergeVariantRequests
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* generated by the resulting import job.
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*/
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infoMergeConfig?: Record<string, string>;
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/**
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* Convert reference names to the canonical representation.
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* hg19 haploytypes (those reference names containing "_hap")
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* are not modified in any way.
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* All other reference names are modified according to the following rules:
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* The reference name is capitalized.
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* The "chr" prefix is dropped for all autosomes and sex chromsomes.
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* For example "chr17" becomes "17" and "chrX" becomes "X".
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* All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
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*/
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normalizeReferenceNames?: boolean;
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/**
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* A list of URIs referencing variant files in Google Cloud Storage. URIs can
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* include wildcards [as described
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* here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
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* Note that recursive wildcards ('**') are not supported.
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*/
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sourceUris?: string[];
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/** Required. The variant set to which variant data should be imported. */
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variantSetId?: string;
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}
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interface ImportVariantsResponse {
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/** IDs of the call sets created during the import. */
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callSetIds?: string[];
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}
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interface LinearAlignment {
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/**
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* Represents the local alignment of this sequence (alignment matches, indels,
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* etc) against the reference.
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*/
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cigar?: CigarUnit[];
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/**
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* The mapping quality of this alignment. Represents how likely
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* the read maps to this position as opposed to other locations.
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*
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* Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
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* the nearest integer.
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*/
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mappingQuality?: number;
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/** The position of this alignment. */
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position?: Position;
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}
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interface ListBasesResponse {
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/**
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* The continuation token, which is used to page through large result sets.
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* Provide this value in a subsequent request to return the next page of
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* results. This field will be empty if there aren't any additional results.
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*/
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nextPageToken?: string;
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/**
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* The offset position (0-based) of the given `sequence` from the
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* start of this `Reference`. This value will differ for each page
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* in a paginated request.
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*/
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offset?: string;
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/** A substring of the bases that make up this reference. */
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sequence?: string;
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}
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interface ListCoverageBucketsResponse {
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/**
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* The length of each coverage bucket in base pairs. Note that buckets at the
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* end of a reference sequence may be shorter. This value is omitted if the
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* bucket width is infinity (the default behaviour, with no range or
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* `targetBucketWidth`).
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*/
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bucketWidth?: string;
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/**
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* The coverage buckets. The list of buckets is sparse; a bucket with 0
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* overlapping reads is not returned. A bucket never crosses more than one
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* reference sequence. Each bucket has width `bucketWidth`, unless
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* its end is the end of the reference sequence.
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*/
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coverageBuckets?: CoverageBucket[];
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/**
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* The continuation token, which is used to page through large result sets.
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* Provide this value in a subsequent request to return the next page of
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* results. This field will be empty if there aren't any additional results.
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*/
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nextPageToken?: string;
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}
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interface ListDatasetsResponse {
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/** The list of matching Datasets. */
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datasets?: Dataset[];
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/**
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* The continuation token, which is used to page through large result sets.
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* Provide this value in a subsequent request to return the next page of
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* results. This field will be empty if there aren't any additional results.
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*/
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nextPageToken?: string;
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}
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interface ListOperationsResponse {
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/** The standard List next-page token. */
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nextPageToken?: string;
|
|
/** A list of operations that matches the specified filter in the request. */
|
|
operations?: Operation[];
|
|
}
|
|
interface MergeVariantsRequest {
|
|
/**
|
|
* A mapping between info field keys and the InfoMergeOperations to
|
|
* be performed on them.
|
|
*/
|
|
infoMergeConfig?: Record<string, string>;
|
|
/** The destination variant set. */
|
|
variantSetId?: string;
|
|
/** The variants to be merged with existing variants. */
|
|
variants?: Variant[];
|
|
}
|
|
interface Operation {
|
|
/**
|
|
* If the value is `false`, it means the operation is still in progress.
|
|
* If `true`, the operation is completed, and either `error` or `response` is
|
|
* available.
|
|
*/
|
|
done?: boolean;
|
|
/** The error result of the operation in case of failure or cancellation. */
|
|
error?: Status;
|
|
/** An OperationMetadata object. This will always be returned with the Operation. */
|
|
metadata?: Record<string, any>;
|
|
/**
|
|
* The server-assigned name, which is only unique within the same service that originally returns it. For example:
|
|
* `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
|
|
*/
|
|
name?: string;
|
|
/**
|
|
* If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and
|
|
* exports, an Empty response is returned.
|
|
*/
|
|
response?: Record<string, any>;
|
|
}
|
|
interface OperationEvent {
|
|
/** Required description of event. */
|
|
description?: string;
|
|
/**
|
|
* Optional time of when event finished. An event can have a start time and no
|
|
* finish time. If an event has a finish time, there must be a start time.
|
|
*/
|
|
endTime?: string;
|
|
/** Optional time of when event started. */
|
|
startTime?: string;
|
|
}
|
|
interface OperationMetadata {
|
|
/**
|
|
* This field is deprecated. Use `labels` instead. Optionally provided by the
|
|
* caller when submitting the request that creates the operation.
|
|
*/
|
|
clientId?: string;
|
|
/** The time at which the job was submitted to the Genomics service. */
|
|
createTime?: string;
|
|
/** The time at which the job stopped running. */
|
|
endTime?: string;
|
|
/**
|
|
* Optional event messages that were generated during the job's execution.
|
|
* This also contains any warnings that were generated during import
|
|
* or export.
|
|
*/
|
|
events?: OperationEvent[];
|
|
/**
|
|
* Optionally provided by the caller when submitting the request that creates
|
|
* the operation.
|
|
*/
|
|
labels?: Record<string, string>;
|
|
/** The Google Cloud Project in which the job is scoped. */
|
|
projectId?: string;
|
|
/**
|
|
* The original request that started the operation. Note that this will be in
|
|
* current version of the API. If the operation was started with v1beta2 API
|
|
* and a GetOperation is performed on v1 API, a v1 request will be returned.
|
|
*/
|
|
request?: Record<string, any>;
|
|
/** Runtime metadata on this Operation. */
|
|
runtimeMetadata?: Record<string, any>;
|
|
/** The time at which the job began to run. */
|
|
startTime?: string;
|
|
}
|
|
interface Policy {
|
|
/**
|
|
* Associates a list of `members` to a `role`.
|
|
* `bindings` with no members will result in an error.
|
|
*/
|
|
bindings?: Binding[];
|
|
/**
|
|
* `etag` is used for optimistic concurrency control as a way to help
|
|
* prevent simultaneous updates of a policy from overwriting each other.
|
|
* It is strongly suggested that systems make use of the `etag` in the
|
|
* read-modify-write cycle to perform policy updates in order to avoid race
|
|
* conditions: An `etag` is returned in the response to `getIamPolicy`, and
|
|
* systems are expected to put that etag in the request to `setIamPolicy` to
|
|
* ensure that their change will be applied to the same version of the policy.
|
|
*
|
|
* If no `etag` is provided in the call to `setIamPolicy`, then the existing
|
|
* policy is overwritten blindly.
|
|
*/
|
|
etag?: string;
|
|
/** Version of the `Policy`. The default version is 0. */
|
|
version?: number;
|
|
}
|
|
interface Position {
|
|
/** The 0-based offset from the start of the forward strand for that reference. */
|
|
position?: string;
|
|
/** The name of the reference in whatever reference set is being used. */
|
|
referenceName?: string;
|
|
/**
|
|
* Whether this position is on the reverse strand, as opposed to the forward
|
|
* strand.
|
|
*/
|
|
reverseStrand?: boolean;
|
|
}
|
|
interface Program {
|
|
/** The command line used to run this program. */
|
|
commandLine?: string;
|
|
/**
|
|
* The user specified locally unique ID of the program. Used along with
|
|
* `prevProgramId` to define an ordering between programs.
|
|
*/
|
|
id?: string;
|
|
/**
|
|
* The display name of the program. This is typically the colloquial name of
|
|
* the tool used, for example 'bwa' or 'picard'.
|
|
*/
|
|
name?: string;
|
|
/** The ID of the program run before this one. */
|
|
prevProgramId?: string;
|
|
/** The version of the program run. */
|
|
version?: string;
|
|
}
|
|
interface Range {
|
|
/** The end position of the range on the reference, 0-based exclusive. */
|
|
end?: string;
|
|
/**
|
|
* The reference sequence name, for example `chr1`,
|
|
* `1`, or `chrX`.
|
|
*/
|
|
referenceName?: string;
|
|
/** The start position of the range on the reference, 0-based inclusive. */
|
|
start?: string;
|
|
}
|
|
interface Read {
|
|
/**
|
|
* The quality of the read sequence contained in this alignment record
|
|
* (equivalent to QUAL in SAM).
|
|
* `alignedSequence` and `alignedQuality` may be shorter than the full read
|
|
* sequence and quality. This will occur if the alignment is part of a
|
|
* chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
|
|
* for this read will begin/end with a hard clip operator that will indicate
|
|
* the length of the excised sequence.
|
|
*/
|
|
alignedQuality?: number[];
|
|
/**
|
|
* The bases of the read sequence contained in this alignment record,
|
|
* **without CIGAR operations applied** (equivalent to SEQ in SAM).
|
|
* `alignedSequence` and `alignedQuality` may be
|
|
* shorter than the full read sequence and quality. This will occur if the
|
|
* alignment is part of a chimeric alignment, or if the read was trimmed. When
|
|
* this occurs, the CIGAR for this read will begin/end with a hard clip
|
|
* operator that will indicate the length of the excised sequence.
|
|
*/
|
|
alignedSequence?: string;
|
|
/**
|
|
* The linear alignment for this alignment record. This field is null for
|
|
* unmapped reads.
|
|
*/
|
|
alignment?: LinearAlignment;
|
|
/** The fragment is a PCR or optical duplicate (SAM flag 0x400). */
|
|
duplicateFragment?: boolean;
|
|
/**
|
|
* Whether this read did not pass filters, such as platform or vendor quality
|
|
* controls (SAM flag 0x200).
|
|
*/
|
|
failedVendorQualityChecks?: boolean;
|
|
/** The observed length of the fragment, equivalent to TLEN in SAM. */
|
|
fragmentLength?: number;
|
|
/** The fragment name. Equivalent to QNAME (query template name) in SAM. */
|
|
fragmentName?: string;
|
|
/**
|
|
* The server-generated read ID, unique across all reads. This is different
|
|
* from the `fragmentName`.
|
|
*/
|
|
id?: string;
|
|
/**
|
|
* A map of additional read alignment information. This must be of the form
|
|
* map<string, string[]> (string key mapping to a list of string values).
|
|
*/
|
|
info?: Record<string, any[]>;
|
|
/**
|
|
* The mapping of the primary alignment of the
|
|
* `(readNumber+1)%numberReads` read in the fragment. It replaces
|
|
* mate position and mate strand in SAM.
|
|
*/
|
|
nextMatePosition?: Position;
|
|
/** The number of reads in the fragment (extension to SAM flag 0x1). */
|
|
numberReads?: number;
|
|
/**
|
|
* The orientation and the distance between reads from the fragment are
|
|
* consistent with the sequencing protocol (SAM flag 0x2).
|
|
*/
|
|
properPlacement?: boolean;
|
|
/**
|
|
* The ID of the read group this read belongs to. A read belongs to exactly
|
|
* one read group. This is a server-generated ID which is distinct from SAM's
|
|
* RG tag (for that value, see
|
|
* ReadGroup.name).
|
|
*/
|
|
readGroupId?: string;
|
|
/**
|
|
* The ID of the read group set this read belongs to. A read belongs to
|
|
* exactly one read group set.
|
|
*/
|
|
readGroupSetId?: string;
|
|
/**
|
|
* The read number in sequencing. 0-based and less than numberReads. This
|
|
* field replaces SAM flag 0x40 and 0x80.
|
|
*/
|
|
readNumber?: number;
|
|
/**
|
|
* Whether this alignment is secondary. Equivalent to SAM flag 0x100.
|
|
* A secondary alignment represents an alternative to the primary alignment
|
|
* for this read. Aligners may return secondary alignments if a read can map
|
|
* ambiguously to multiple coordinates in the genome. By convention, each read
|
|
* has one and only one alignment where both `secondaryAlignment`
|
|
* and `supplementaryAlignment` are false.
|
|
*/
|
|
secondaryAlignment?: boolean;
|
|
/**
|
|
* Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
|
|
* Supplementary alignments are used in the representation of a chimeric
|
|
* alignment. In a chimeric alignment, a read is split into multiple
|
|
* linear alignments that map to different reference contigs. The first
|
|
* linear alignment in the read will be designated as the representative
|
|
* alignment; the remaining linear alignments will be designated as
|
|
* supplementary alignments. These alignments may have different mapping
|
|
* quality scores. In each linear alignment in a chimeric alignment, the read
|
|
* will be hard clipped. The `alignedSequence` and
|
|
* `alignedQuality` fields in the alignment record will only
|
|
* represent the bases for its respective linear alignment.
|
|
*/
|
|
supplementaryAlignment?: boolean;
|
|
}
|
|
interface ReadGroup {
|
|
/** The dataset to which this read group belongs. */
|
|
datasetId?: string;
|
|
/** A free-form text description of this read group. */
|
|
description?: string;
|
|
/** The experiment used to generate this read group. */
|
|
experiment?: Experiment;
|
|
/**
|
|
* The server-generated read group ID, unique for all read groups.
|
|
* Note: This is different than the @RG ID field in the SAM spec. For that
|
|
* value, see name.
|
|
*/
|
|
id?: string;
|
|
/**
|
|
* A map of additional read group information. This must be of the form
|
|
* map<string, string[]> (string key mapping to a list of string values).
|
|
*/
|
|
info?: Record<string, any[]>;
|
|
/** The read group name. This corresponds to the @RG ID field in the SAM spec. */
|
|
name?: string;
|
|
/**
|
|
* The predicted insert size of this read group. The insert size is the length
|
|
* the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
*/
|
|
predictedInsertSize?: number;
|
|
/**
|
|
* The programs used to generate this read group. Programs are always
|
|
* identical for all read groups within a read group set. For this reason,
|
|
* only the first read group in a returned set will have this field
|
|
* populated.
|
|
*/
|
|
programs?: Program[];
|
|
/** The reference set the reads in this read group are aligned to. */
|
|
referenceSetId?: string;
|
|
/** A client-supplied sample identifier for the reads in this read group. */
|
|
sampleId?: string;
|
|
}
|
|
interface ReadGroupSet {
|
|
/** The dataset to which this read group set belongs. */
|
|
datasetId?: string;
|
|
/** The filename of the original source file for this read group set, if any. */
|
|
filename?: string;
|
|
/** The server-generated read group set ID, unique for all read group sets. */
|
|
id?: string;
|
|
/** A map of additional read group set information. */
|
|
info?: Record<string, any[]>;
|
|
/**
|
|
* The read group set name. By default this will be initialized to the sample
|
|
* name of the sequenced data contained in this set.
|
|
*/
|
|
name?: string;
|
|
/**
|
|
* The read groups in this set. There are typically 1-10 read groups in a read
|
|
* group set.
|
|
*/
|
|
readGroups?: ReadGroup[];
|
|
/** The reference set to which the reads in this read group set are aligned. */
|
|
referenceSetId?: string;
|
|
}
|
|
interface Reference {
|
|
/** The server-generated reference ID, unique across all references. */
|
|
id?: string;
|
|
/** The length of this reference's sequence. */
|
|
length?: string;
|
|
/**
|
|
* MD5 of the upper-case sequence excluding all whitespace characters (this
|
|
* is equivalent to SQ:M5 in SAM). This value is represented in lower case
|
|
* hexadecimal format.
|
|
*/
|
|
md5checksum?: string;
|
|
/** The name of this reference, for example `22`. */
|
|
name?: string;
|
|
/** ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human. */
|
|
ncbiTaxonId?: number;
|
|
/**
|
|
* All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
|
* with a version number, for example `GCF_000001405.26`.
|
|
*/
|
|
sourceAccessions?: string[];
|
|
/**
|
|
* The URI from which the sequence was obtained. Typically specifies a FASTA
|
|
* format file.
|
|
*/
|
|
sourceUri?: string;
|
|
}
|
|
interface ReferenceBound {
|
|
/** The name of the reference associated with this reference bound. */
|
|
referenceName?: string;
|
|
/**
|
|
* An upper bound (inclusive) on the starting coordinate of any
|
|
* variant in the reference sequence.
|
|
*/
|
|
upperBound?: string;
|
|
}
|
|
interface ReferenceSet {
|
|
/** Public id of this reference set, such as `GRCh37`. */
|
|
assemblyId?: string;
|
|
/** Free text description of this reference set. */
|
|
description?: string;
|
|
/** The server-generated reference set ID, unique across all reference sets. */
|
|
id?: string;
|
|
/**
|
|
* Order-independent MD5 checksum which identifies this reference set. The
|
|
* checksum is computed by sorting all lower case hexidecimal string
|
|
* `reference.md5checksum` (for all reference in this set) in
|
|
* ascending lexicographic order, concatenating, and taking the MD5 of that
|
|
* value. The resulting value is represented in lower case hexadecimal format.
|
|
*/
|
|
md5checksum?: string;
|
|
/**
|
|
* ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
|
|
* indicating the species which this reference set is intended to model. Note
|
|
* that contained references may specify a different `ncbiTaxonId`, as
|
|
* assemblies may contain reference sequences which do not belong to the
|
|
* modeled species, for example EBV in a human reference genome.
|
|
*/
|
|
ncbiTaxonId?: number;
|
|
/**
|
|
* The IDs of the reference objects that are part of this set.
|
|
* `Reference.md5checksum` must be unique within this set.
|
|
*/
|
|
referenceIds?: string[];
|
|
/**
|
|
* All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
|
* with a version number, for example `NC_000001.11`.
|
|
*/
|
|
sourceAccessions?: string[];
|
|
/** The URI from which the references were obtained. */
|
|
sourceUri?: string;
|
|
}
|
|
interface RuntimeMetadata {
|
|
/** Execution information specific to Google Compute Engine. */
|
|
computeEngine?: ComputeEngine;
|
|
}
|
|
interface SearchAnnotationSetsRequest {
|
|
/**
|
|
* Required. The dataset IDs to search within. Caller must have `READ` access
|
|
* to these datasets.
|
|
*/
|
|
datasetIds?: string[];
|
|
/**
|
|
* Only return annotations sets for which a substring of the name matches this
|
|
* string (case insensitive).
|
|
*/
|
|
name?: string;
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 128. The maximum value is 1024.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/**
|
|
* If specified, only annotation sets associated with the given reference set
|
|
* are returned.
|
|
*/
|
|
referenceSetId?: string;
|
|
/**
|
|
* If specified, only annotation sets that have any of these types are
|
|
* returned.
|
|
*/
|
|
types?: string[];
|
|
}
|
|
interface SearchAnnotationSetsResponse {
|
|
/** The matching annotation sets. */
|
|
annotationSets?: AnnotationSet[];
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
}
|
|
interface SearchAnnotationsRequest {
|
|
/**
|
|
* Required. The annotation sets to search within. The caller must have
|
|
* `READ` access to these annotation sets.
|
|
* All queried annotation sets must have the same type.
|
|
*/
|
|
annotationSetIds?: string[];
|
|
/**
|
|
* The end position of the range on the reference, 0-based exclusive. If
|
|
* referenceId or
|
|
* referenceName
|
|
* must be specified, Defaults to the length of the reference.
|
|
*/
|
|
end?: string;
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 256. The maximum value is 2048.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/** The ID of the reference to query. */
|
|
referenceId?: string;
|
|
/**
|
|
* The name of the reference to query, within the reference set associated
|
|
* with this query.
|
|
*/
|
|
referenceName?: string;
|
|
/**
|
|
* The start position of the range on the reference, 0-based inclusive. If
|
|
* specified,
|
|
* referenceId or
|
|
* referenceName
|
|
* must be specified. Defaults to 0.
|
|
*/
|
|
start?: string;
|
|
}
|
|
interface SearchAnnotationsResponse {
|
|
/** The matching annotations. */
|
|
annotations?: Annotation[];
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
}
|
|
interface SearchCallSetsRequest {
|
|
/**
|
|
* Only return call sets for which a substring of the name matches this
|
|
* string.
|
|
*/
|
|
name?: string;
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 1024.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/**
|
|
* Restrict the query to call sets within the given variant sets. At least one
|
|
* ID must be provided.
|
|
*/
|
|
variantSetIds?: string[];
|
|
}
|
|
interface SearchCallSetsResponse {
|
|
/** The list of matching call sets. */
|
|
callSets?: CallSet[];
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
}
|
|
interface SearchReadGroupSetsRequest {
|
|
/**
|
|
* Restricts this query to read group sets within the given datasets. At least
|
|
* one ID must be provided.
|
|
*/
|
|
datasetIds?: string[];
|
|
/**
|
|
* Only return read group sets for which a substring of the name matches this
|
|
* string.
|
|
*/
|
|
name?: string;
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 256. The maximum value is 1024.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
}
|
|
interface SearchReadGroupSetsResponse {
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
/** The list of matching read group sets. */
|
|
readGroupSets?: ReadGroupSet[];
|
|
}
|
|
interface SearchReadsRequest {
|
|
/**
|
|
* The end position of the range on the reference, 0-based exclusive. If
|
|
* specified, `referenceName` must also be specified.
|
|
*/
|
|
end?: string;
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 256. The maximum value is 2048.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/**
|
|
* The IDs of the read groups within which to search for reads. All specified
|
|
* read groups must belong to the same read group sets. Must specify one of
|
|
* `readGroupSetIds` or `readGroupIds`.
|
|
*/
|
|
readGroupIds?: string[];
|
|
/**
|
|
* The IDs of the read groups sets within which to search for reads. All
|
|
* specified read group sets must be aligned against a common set of reference
|
|
* sequences; this defines the genomic coordinates for the query. Must specify
|
|
* one of `readGroupSetIds` or `readGroupIds`.
|
|
*/
|
|
readGroupSetIds?: string[];
|
|
/**
|
|
* The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
|
|
* `*`, only unmapped reads are returned. If unspecified, all reads (mapped
|
|
* and unmapped) are returned.
|
|
*/
|
|
referenceName?: string;
|
|
/**
|
|
* The start position of the range on the reference, 0-based inclusive. If
|
|
* specified, `referenceName` must also be specified.
|
|
*/
|
|
start?: string;
|
|
}
|
|
interface SearchReadsResponse {
|
|
/**
|
|
* The list of matching alignments sorted by mapped genomic coordinate,
|
|
* if any, ascending in position within the same reference. Unmapped reads,
|
|
* which have no position, are returned contiguously and are sorted in
|
|
* ascending lexicographic order by fragment name.
|
|
*/
|
|
alignments?: Read[];
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
}
|
|
interface SearchReferenceSetsRequest {
|
|
/**
|
|
* If present, return reference sets for which a prefix of any of
|
|
* sourceAccessions
|
|
* match any of these strings. Accession numbers typically have a main number
|
|
* and a version, for example `NC_000001.11`.
|
|
*/
|
|
accessions?: string[];
|
|
/**
|
|
* If present, return reference sets for which a substring of their
|
|
* `assemblyId` matches this string (case insensitive).
|
|
*/
|
|
assemblyId?: string;
|
|
/**
|
|
* If present, return reference sets for which the
|
|
* md5checksum matches exactly.
|
|
*/
|
|
md5checksums?: string[];
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 1024. The maximum value is 4096.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
}
|
|
interface SearchReferenceSetsResponse {
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
/** The matching references sets. */
|
|
referenceSets?: ReferenceSet[];
|
|
}
|
|
interface SearchReferencesRequest {
|
|
/**
|
|
* If present, return references for which a prefix of any of
|
|
* sourceAccessions match
|
|
* any of these strings. Accession numbers typically have a main number and a
|
|
* version, for example `GCF_000001405.26`.
|
|
*/
|
|
accessions?: string[];
|
|
/**
|
|
* If present, return references for which the
|
|
* md5checksum matches exactly.
|
|
*/
|
|
md5checksums?: string[];
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 1024. The maximum value is 4096.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/** If present, return only references which belong to this reference set. */
|
|
referenceSetId?: string;
|
|
}
|
|
interface SearchReferencesResponse {
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
/** The matching references. */
|
|
references?: Reference[];
|
|
}
|
|
interface SearchVariantSetsRequest {
|
|
/**
|
|
* Exactly one dataset ID must be provided here. Only variant sets which
|
|
* belong to this dataset will be returned.
|
|
*/
|
|
datasetIds?: string[];
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 1024.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
}
|
|
interface SearchVariantSetsResponse {
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
/** The variant sets belonging to the requested dataset. */
|
|
variantSets?: VariantSet[];
|
|
}
|
|
interface SearchVariantsRequest {
|
|
/**
|
|
* Only return variant calls which belong to call sets with these ids.
|
|
* Leaving this blank returns all variant calls. If a variant has no
|
|
* calls belonging to any of these call sets, it won't be returned at all.
|
|
*/
|
|
callSetIds?: string[];
|
|
/**
|
|
* The end of the window, 0-based exclusive. If unspecified or 0, defaults to
|
|
* the length of the reference.
|
|
*/
|
|
end?: string;
|
|
/**
|
|
* The maximum number of calls to return in a single page. Note that this
|
|
* limit may be exceeded in the event that a matching variant contains more
|
|
* calls than the requested maximum. If unspecified, defaults to 5000. The
|
|
* maximum value is 10000.
|
|
*/
|
|
maxCalls?: number;
|
|
/**
|
|
* The maximum number of variants to return in a single page. If unspecified,
|
|
* defaults to 5000. The maximum value is 10000.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/** Required. Only return variants in this reference sequence. */
|
|
referenceName?: string;
|
|
/**
|
|
* The beginning of the window (0-based, inclusive) for which
|
|
* overlapping variants should be returned. If unspecified, defaults to 0.
|
|
*/
|
|
start?: string;
|
|
/** Only return variants which have exactly this name. */
|
|
variantName?: string;
|
|
/**
|
|
* At most one variant set ID must be provided. Only variants from this
|
|
* variant set will be returned. If omitted, a call set id must be included in
|
|
* the request.
|
|
*/
|
|
variantSetIds?: string[];
|
|
}
|
|
interface SearchVariantsResponse {
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* Provide this value in a subsequent request to return the next page of
|
|
* results. This field will be empty if there aren't any additional results.
|
|
*/
|
|
nextPageToken?: string;
|
|
/** The list of matching Variants. */
|
|
variants?: Variant[];
|
|
}
|
|
interface SetIamPolicyRequest {
|
|
/**
|
|
* REQUIRED: The complete policy to be applied to the `resource`. The size of
|
|
* the policy is limited to a few 10s of KB. An empty policy is a
|
|
* valid policy but certain Cloud Platform services (such as Projects)
|
|
* might reject them.
|
|
*/
|
|
policy?: Policy;
|
|
}
|
|
interface Status {
|
|
/** The status code, which should be an enum value of google.rpc.Code. */
|
|
code?: number;
|
|
/**
|
|
* A list of messages that carry the error details. There is a common set of
|
|
* message types for APIs to use.
|
|
*/
|
|
details?: Array<Record<string, any>>;
|
|
/**
|
|
* A developer-facing error message, which should be in English. Any
|
|
* user-facing error message should be localized and sent in the
|
|
* google.rpc.Status.details field, or localized by the client.
|
|
*/
|
|
message?: string;
|
|
}
|
|
interface TestIamPermissionsRequest {
|
|
/**
|
|
* REQUIRED: The set of permissions to check for the 'resource'.
|
|
* Permissions with wildcards (such as '*' or 'storage.*') are not allowed.
|
|
* Allowed permissions are:
|
|
*
|
|
* * `genomics.datasets.create`
|
|
* * `genomics.datasets.delete`
|
|
* * `genomics.datasets.get`
|
|
* * `genomics.datasets.list`
|
|
* * `genomics.datasets.update`
|
|
* * `genomics.datasets.getIamPolicy`
|
|
* * `genomics.datasets.setIamPolicy`
|
|
*/
|
|
permissions?: string[];
|
|
}
|
|
interface TestIamPermissionsResponse {
|
|
/**
|
|
* A subset of `TestPermissionsRequest.permissions` that the caller is
|
|
* allowed.
|
|
*/
|
|
permissions?: string[];
|
|
}
|
|
interface Transcript {
|
|
/**
|
|
* The range of the coding sequence for this transcript, if any. To determine
|
|
* the exact ranges of coding sequence, intersect this range with those of the
|
|
* exons, if any. If there are any
|
|
* exons, the
|
|
* codingSequence must start
|
|
* and end within them.
|
|
*
|
|
* Note that in some cases, the reference genome will not exactly match the
|
|
* observed mRNA transcript e.g. due to variance in the source genome from
|
|
* reference. In these cases,
|
|
* exon.frame will not necessarily
|
|
* match the expected reference reading frame and coding exon reference bases
|
|
* cannot necessarily be concatenated to produce the original transcript mRNA.
|
|
*/
|
|
codingSequence?: CodingSequence;
|
|
/**
|
|
* The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose
|
|
* this transcript. This field should be unset for genomes where transcript
|
|
* splicing does not occur, for example prokaryotes.
|
|
*
|
|
* Introns are regions of the transcript that are not included in the
|
|
* spliced RNA product. Though not explicitly modeled here, intron ranges can
|
|
* be deduced; all regions of this transcript that are not exons are introns.
|
|
*
|
|
* Exonic sequences do not necessarily code for a translational product
|
|
* (amino acids). Only the regions of exons bounded by the
|
|
* codingSequence correspond
|
|
* to coding DNA sequence.
|
|
*
|
|
* Exons are ordered by start position and may not overlap.
|
|
*/
|
|
exons?: Exon[];
|
|
/** The annotation ID of the gene from which this transcript is transcribed. */
|
|
geneId?: string;
|
|
}
|
|
interface Variant {
|
|
/** The bases that appear instead of the reference bases. */
|
|
alternateBases?: string[];
|
|
/**
|
|
* The variant calls for this particular variant. Each one represents the
|
|
* determination of genotype with respect to this variant.
|
|
*/
|
|
calls?: VariantCall[];
|
|
/** The date this variant was created, in milliseconds from the epoch. */
|
|
created?: string;
|
|
/**
|
|
* The end position (0-based) of this variant. This corresponds to the first
|
|
* base after the last base in the reference allele. So, the length of
|
|
* the reference allele is (end - start). This is useful for variants
|
|
* that don't explicitly give alternate bases, for example large deletions.
|
|
*/
|
|
end?: string;
|
|
/**
|
|
* A list of filters (normally quality filters) this variant has failed.
|
|
* `PASS` indicates this variant has passed all filters.
|
|
*/
|
|
filter?: string[];
|
|
/** The server-generated variant ID, unique across all variants. */
|
|
id?: string;
|
|
/**
|
|
* A map of additional variant information. This must be of the form
|
|
* map<string, string[]> (string key mapping to a list of string values).
|
|
*/
|
|
info?: Record<string, any[]>;
|
|
/** Names for the variant, for example a RefSNP ID. */
|
|
names?: string[];
|
|
/**
|
|
* A measure of how likely this variant is to be real.
|
|
* A higher value is better.
|
|
*/
|
|
quality?: number;
|
|
/**
|
|
* The reference bases for this variant. They start at the given
|
|
* position.
|
|
*/
|
|
referenceBases?: string;
|
|
/**
|
|
* The reference on which this variant occurs.
|
|
* (such as `chr20` or `X`)
|
|
*/
|
|
referenceName?: string;
|
|
/**
|
|
* The position at which this variant occurs (0-based).
|
|
* This corresponds to the first base of the string of reference bases.
|
|
*/
|
|
start?: string;
|
|
/** The ID of the variant set this variant belongs to. */
|
|
variantSetId?: string;
|
|
}
|
|
interface VariantAnnotation {
|
|
/**
|
|
* The alternate allele for this variant. If multiple alternate alleles
|
|
* exist at this location, create a separate variant for each one, as they
|
|
* may represent distinct conditions.
|
|
*/
|
|
alternateBases?: string;
|
|
/**
|
|
* Describes the clinical significance of a variant.
|
|
* It is adapted from the ClinVar controlled vocabulary for clinical
|
|
* significance described at:
|
|
* http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
|
|
*/
|
|
clinicalSignificance?: string;
|
|
/**
|
|
* The set of conditions associated with this variant.
|
|
* A condition describes the way a variant influences human health.
|
|
*/
|
|
conditions?: ClinicalCondition[];
|
|
/** Effect of the variant on the coding sequence. */
|
|
effect?: string;
|
|
/**
|
|
* Google annotation ID of the gene affected by this variant. This should
|
|
* be provided when the variant is created.
|
|
*/
|
|
geneId?: string;
|
|
/**
|
|
* Google annotation IDs of the transcripts affected by this variant. These
|
|
* should be provided when the variant is created.
|
|
*/
|
|
transcriptIds?: string[];
|
|
/** Type has been adapted from ClinVar's list of variant types. */
|
|
type?: string;
|
|
}
|
|
interface VariantCall {
|
|
/** The ID of the call set this variant call belongs to. */
|
|
callSetId?: string;
|
|
/** The name of the call set this variant call belongs to. */
|
|
callSetName?: string;
|
|
/**
|
|
* The genotype of this variant call. Each value represents either the value
|
|
* of the `referenceBases` field or a 1-based index into
|
|
* `alternateBases`. If a variant had a `referenceBases`
|
|
* value of `T` and an `alternateBases`
|
|
* value of `["A", "C"]`, and the `genotype` was
|
|
* `[2, 1]`, that would mean the call
|
|
* represented the heterozygous value `CA` for this variant.
|
|
* If the `genotype` was instead `[0, 1]`, the
|
|
* represented value would be `TA`. Ordering of the
|
|
* genotype values is important if the `phaseset` is present.
|
|
* If a genotype is not called (that is, a `.` is present in the
|
|
* GT string) -1 is returned.
|
|
*/
|
|
genotype?: number[];
|
|
/**
|
|
* The genotype likelihoods for this variant call. Each array entry
|
|
* represents how likely a specific genotype is for this call. The value
|
|
* ordering is defined by the GL tag in the VCF spec.
|
|
* If Phred-scaled genotype likelihood scores (PL) are available and
|
|
* log10(P) genotype likelihood scores (GL) are not, PL scores are converted
|
|
* to GL scores. If both are available, PL scores are stored in `info`.
|
|
*/
|
|
genotypeLikelihood?: number[];
|
|
/**
|
|
* A map of additional variant call information. This must be of the form
|
|
* map<string, string[]> (string key mapping to a list of string values).
|
|
*/
|
|
info?: Record<string, any[]>;
|
|
/**
|
|
* If this field is present, this variant call's genotype ordering implies
|
|
* the phase of the bases and is consistent with any other variant calls in
|
|
* the same reference sequence which have the same phaseset value.
|
|
* When importing data from VCF, if the genotype data was phased but no
|
|
* phase set was specified this field will be set to `*`.
|
|
*/
|
|
phaseset?: string;
|
|
}
|
|
interface VariantSet {
|
|
/** The dataset to which this variant set belongs. */
|
|
datasetId?: string;
|
|
/** A textual description of this variant set. */
|
|
description?: string;
|
|
/** The server-generated variant set ID, unique across all variant sets. */
|
|
id?: string;
|
|
/** The metadata associated with this variant set. */
|
|
metadata?: VariantSetMetadata[];
|
|
/** User-specified, mutable name. */
|
|
name?: string;
|
|
/**
|
|
* A list of all references used by the variants in a variant set
|
|
* with associated coordinate upper bounds for each one.
|
|
*/
|
|
referenceBounds?: ReferenceBound[];
|
|
/**
|
|
* The reference set to which the variant set is mapped. The reference set
|
|
* describes the alignment provenance of the variant set, while the
|
|
* `referenceBounds` describe the shape of the actual variant data. The
|
|
* reference set's reference names are a superset of those found in the
|
|
* `referenceBounds`.
|
|
*
|
|
* For example, given a variant set that is mapped to the GRCh38 reference set
|
|
* and contains a single variant on reference 'X', `referenceBounds` would
|
|
* contain only an entry for 'X', while the associated reference set
|
|
* enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
|
|
*/
|
|
referenceSetId?: string;
|
|
}
|
|
interface VariantSetMetadata {
|
|
/** A textual description of this metadata. */
|
|
description?: string;
|
|
/**
|
|
* User-provided ID field, not enforced by this API.
|
|
* Two or more pieces of structured metadata with identical
|
|
* id and key fields are considered equivalent.
|
|
*/
|
|
id?: string;
|
|
/**
|
|
* Remaining structured metadata key-value pairs. This must be of the form
|
|
* map<string, string[]> (string key mapping to a list of string values).
|
|
*/
|
|
info?: Record<string, any[]>;
|
|
/** The top-level key. */
|
|
key?: string;
|
|
/**
|
|
* The number of values that can be included in a field described by this
|
|
* metadata.
|
|
*/
|
|
number?: string;
|
|
/**
|
|
* The type of data. Possible types include: Integer, Float,
|
|
* Flag, Character, and String.
|
|
*/
|
|
type?: string;
|
|
/** The value field for simple metadata */
|
|
value?: string;
|
|
}
|
|
interface AnnotationsResource {
|
|
/**
|
|
* Creates one or more new annotations atomically. All annotations must
|
|
* belong to the same annotation set. Caller must have WRITE
|
|
* permission for this annotation set. For optimal performance, batch
|
|
* positionally adjacent annotations together.
|
|
*
|
|
* If the request has a systemic issue, such as an attempt to write to
|
|
* an inaccessible annotation set, the entire RPC will fail accordingly. For
|
|
* lesser data issues, when possible an error will be isolated to the
|
|
* corresponding batch entry in the response; the remaining well formed
|
|
* annotations will be created normally.
|
|
*
|
|
* For details on the requirements for each individual annotation resource,
|
|
* see
|
|
* CreateAnnotation.
|
|
*/
|
|
batchCreate(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<BatchCreateAnnotationsResponse>;
|
|
/**
|
|
* Creates a new annotation. Caller must have WRITE permission
|
|
* for the associated annotation set.
|
|
*
|
|
* The following fields are required:
|
|
*
|
|
* * annotationSetId
|
|
* * referenceName or
|
|
* referenceId
|
|
*
|
|
* ### Transcripts
|
|
*
|
|
* For annotations of type TRANSCRIPT, the following fields of
|
|
* transcript must be provided:
|
|
*
|
|
* * exons.start
|
|
* * exons.end
|
|
*
|
|
* All other fields may be optionally specified, unless documented as being
|
|
* server-generated (for example, the `id` field). The annotated
|
|
* range must be no longer than 100Mbp (mega base pairs). See the
|
|
* Annotation resource
|
|
* for additional restrictions on each field.
|
|
*/
|
|
create(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Annotation>;
|
|
/**
|
|
* Deletes an annotation. Caller must have WRITE permission for
|
|
* the associated annotation set.
|
|
*/
|
|
delete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** The ID of the annotation to be deleted. */
|
|
annotationId: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Gets an annotation. Caller must have READ permission
|
|
* for the associated annotation set.
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** The ID of the annotation to be retrieved. */
|
|
annotationId: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Annotation>;
|
|
/**
|
|
* Searches for annotations that match the given criteria. Results are
|
|
* ordered by genomic coordinate (by reference sequence, then position).
|
|
* Annotations with equivalent genomic coordinates are returned in an
|
|
* unspecified order. This order is consistent, such that two queries for the
|
|
* same content (regardless of page size) yield annotations in the same order
|
|
* across their respective streams of paginated responses. Caller must have
|
|
* READ permission for the queried annotation sets.
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchAnnotationsResponse>;
|
|
/**
|
|
* Updates an annotation. Caller must have
|
|
* WRITE permission for the associated dataset.
|
|
*/
|
|
update(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** The ID of the annotation to be updated. */
|
|
annotationId: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* An optional mask specifying which fields to update. Mutable fields are
|
|
* name,
|
|
* variant,
|
|
* transcript, and
|
|
* info. If unspecified, all mutable
|
|
* fields will be updated.
|
|
*/
|
|
updateMask?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Annotation>;
|
|
}
|
|
interface AnnotationsetsResource {
|
|
/**
|
|
* Creates a new annotation set. Caller must have WRITE permission for the
|
|
* associated dataset.
|
|
*
|
|
* The following fields are required:
|
|
*
|
|
* * datasetId
|
|
* * referenceSetId
|
|
*
|
|
* All other fields may be optionally specified, unless documented as being
|
|
* server-generated (for example, the `id` field).
|
|
*/
|
|
create(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<AnnotationSet>;
|
|
/**
|
|
* Deletes an annotation set. Caller must have WRITE permission
|
|
* for the associated annotation set.
|
|
*/
|
|
delete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** The ID of the annotation set to be deleted. */
|
|
annotationSetId: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Gets an annotation set. Caller must have READ permission for
|
|
* the associated dataset.
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** The ID of the annotation set to be retrieved. */
|
|
annotationSetId: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<AnnotationSet>;
|
|
/**
|
|
* Searches for annotation sets that match the given criteria. Annotation sets
|
|
* are returned in an unspecified order. This order is consistent, such that
|
|
* two queries for the same content (regardless of page size) yield annotation
|
|
* sets in the same order across their respective streams of paginated
|
|
* responses. Caller must have READ permission for the queried datasets.
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchAnnotationSetsResponse>;
|
|
/**
|
|
* Updates an annotation set. The update must respect all mutability
|
|
* restrictions and other invariants described on the annotation set resource.
|
|
* Caller must have WRITE permission for the associated dataset.
|
|
*/
|
|
update(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** The ID of the annotation set to be updated. */
|
|
annotationSetId: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* An optional mask specifying which fields to update. Mutable fields are
|
|
* name,
|
|
* source_uri, and
|
|
* info. If unspecified, all
|
|
* mutable fields will be updated.
|
|
*/
|
|
updateMask?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<AnnotationSet>;
|
|
}
|
|
interface CallsetsResource {
|
|
/**
|
|
* Creates a new call set.
|
|
*
|
|
* For the definitions of call sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
create(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<CallSet>;
|
|
/**
|
|
* Deletes a call set.
|
|
*
|
|
* For the definitions of call sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
delete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** The ID of the call set to be deleted. */
|
|
callSetId: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Gets a call set by ID.
|
|
*
|
|
* For the definitions of call sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** The ID of the call set. */
|
|
callSetId: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<CallSet>;
|
|
/**
|
|
* Updates a call set.
|
|
*
|
|
* For the definitions of call sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* This method supports patch semantics.
|
|
*/
|
|
patch(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** The ID of the call set to be updated. */
|
|
callSetId: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* An optional mask specifying which fields to update. At this time, the only
|
|
* mutable field is name. The only
|
|
* acceptable value is "name". If unspecified, all mutable fields will be
|
|
* updated.
|
|
*/
|
|
updateMask?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<CallSet>;
|
|
/**
|
|
* Gets a list of call sets matching the criteria.
|
|
*
|
|
* For the definitions of call sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchCallSetsResponse>;
|
|
}
|
|
interface DatasetsResource {
|
|
/**
|
|
* Creates a new dataset.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
create(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Dataset>;
|
|
/**
|
|
* Deletes a dataset and all of its contents (all read group sets,
|
|
* reference sets, variant sets, call sets, annotation sets, etc.)
|
|
* This is reversible (up to one week after the deletion) via
|
|
* the
|
|
* datasets.undelete
|
|
* operation.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
delete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** The ID of the dataset to be deleted. */
|
|
datasetId: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Gets a dataset by ID.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** The ID of the dataset. */
|
|
datasetId: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Dataset>;
|
|
/**
|
|
* Gets the access control policy for the dataset. This is empty if the
|
|
* policy or resource does not exist.
|
|
*
|
|
* See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
|
|
* Policy</a> for more information.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
getIamPolicy(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* REQUIRED: The resource for which policy is being specified. Format is
|
|
* `datasets/<dataset ID>`.
|
|
*/
|
|
resource: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Policy>;
|
|
/**
|
|
* Lists datasets within a project.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
list(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 50. The maximum value is 1024.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Required. The Google Cloud project ID to list datasets for. */
|
|
projectId?: string;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<ListDatasetsResponse>;
|
|
/**
|
|
* Updates a dataset.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* This method supports patch semantics.
|
|
*/
|
|
patch(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** The ID of the dataset to be updated. */
|
|
datasetId: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* An optional mask specifying which fields to update. At this time, the only
|
|
* mutable field is name. The only
|
|
* acceptable value is "name". If unspecified, all mutable fields will be
|
|
* updated.
|
|
*/
|
|
updateMask?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Dataset>;
|
|
/**
|
|
* Sets the access control policy on the specified dataset. Replaces any
|
|
* existing policy.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
|
|
* Policy</a> for more information.
|
|
*/
|
|
setIamPolicy(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* REQUIRED: The resource for which policy is being specified. Format is
|
|
* `datasets/<dataset ID>`.
|
|
*/
|
|
resource: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Policy>;
|
|
/**
|
|
* Returns permissions that a caller has on the specified resource.
|
|
* See <a href="/iam/docs/managing-policies#testing_permissions">Testing
|
|
* Permissions</a> for more information.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
testIamPermissions(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* REQUIRED: The resource for which policy is being specified. Format is
|
|
* `datasets/<dataset ID>`.
|
|
*/
|
|
resource: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<TestIamPermissionsResponse>;
|
|
/**
|
|
* Undeletes a dataset by restoring a dataset which was deleted via this API.
|
|
*
|
|
* For the definitions of datasets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* This operation is only possible for a week after the deletion occurred.
|
|
*/
|
|
undelete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** The ID of the dataset to be undeleted. */
|
|
datasetId: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Dataset>;
|
|
}
|
|
interface OperationsResource {
|
|
/**
|
|
* Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed.
|
|
* Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite
|
|
* cancellation.
|
|
*/
|
|
cancel(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** The name of the operation resource to be cancelled. */
|
|
name: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Gets the latest state of a long-running operation. Clients can use this
|
|
* method to poll the operation result at intervals as recommended by the API
|
|
* service.
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** The name of the operation resource. */
|
|
name: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Operation>;
|
|
/** Lists operations that match the specified filter in the request. */
|
|
list(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/**
|
|
* A string for filtering Operations.
|
|
* The following filter fields are supported:
|
|
*
|
|
* * projectId: Required. Corresponds to
|
|
* OperationMetadata.projectId.
|
|
* * createTime: The time this job was created, in seconds from the
|
|
* [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
|
|
* operators.
|
|
* * status: Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
|
|
* one status may be specified.
|
|
* * labels.key where key is a label key.
|
|
*
|
|
* Examples:
|
|
*
|
|
* * `projectId = my-project AND createTime >= 1432140000`
|
|
* * `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING`
|
|
* * `projectId = my-project AND labels.color = *`
|
|
* * `projectId = my-project AND labels.color = red`
|
|
*/
|
|
filter?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** The name of the operation's parent resource. */
|
|
name: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/**
|
|
* The maximum number of results to return. If unspecified, defaults to
|
|
* 256. The maximum value is 2048.
|
|
*/
|
|
pageSize?: number;
|
|
/** The standard list page token. */
|
|
pageToken?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<ListOperationsResponse>;
|
|
}
|
|
interface CoveragebucketsResource {
|
|
/**
|
|
* Lists fixed width coverage buckets for a read group set, each of which
|
|
* correspond to a range of a reference sequence. Each bucket summarizes
|
|
* coverage information across its corresponding genomic range.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Coverage is defined as the number of reads which are aligned to a given
|
|
* base in the reference sequence. Coverage buckets are available at several
|
|
* precomputed bucket widths, enabling retrieval of various coverage 'zoom
|
|
* levels'. The caller must have READ permissions for the target read group
|
|
* set.
|
|
*/
|
|
list(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/**
|
|
* The end position of the range on the reference, 0-based exclusive. If
|
|
* specified, `referenceName` must also be specified. If unset or 0, defaults
|
|
* to the length of the reference.
|
|
*/
|
|
end?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/**
|
|
* The maximum number of results to return in a single page. If unspecified,
|
|
* defaults to 1024. The maximum value is 2048.
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Required. The ID of the read group set over which coverage is requested. */
|
|
readGroupSetId: string;
|
|
/**
|
|
* The name of the reference to query, within the reference set associated
|
|
* with this query. Optional.
|
|
*/
|
|
referenceName?: string;
|
|
/**
|
|
* The start position of the range on the reference, 0-based inclusive. If
|
|
* specified, `referenceName` must also be specified. Defaults to 0.
|
|
*/
|
|
start?: string;
|
|
/**
|
|
* The desired width of each reported coverage bucket in base pairs. This
|
|
* will be rounded down to the nearest precomputed bucket width; the value
|
|
* of which is returned as `bucketWidth` in the response. Defaults
|
|
* to infinity (each bucket spans an entire reference sequence) or the length
|
|
* of the target range, if specified. The smallest precomputed
|
|
* `bucketWidth` is currently 2048 base pairs; this is subject to
|
|
* change.
|
|
*/
|
|
targetBucketWidth?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<ListCoverageBucketsResponse>;
|
|
}
|
|
interface ReadgroupsetsResource {
|
|
/**
|
|
* Deletes a read group set.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
delete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* The ID of the read group set to be deleted. The caller must have WRITE
|
|
* permissions to the dataset associated with this read group set.
|
|
*/
|
|
readGroupSetId: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Exports a read group set to a BAM file in Google Cloud Storage.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Note that currently there may be some differences between exported BAM
|
|
* files and the original BAM file at the time of import. See
|
|
* ImportReadGroupSets
|
|
* for caveats.
|
|
*/
|
|
export(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* Required. The ID of the read group set to export. The caller must have
|
|
* READ access to this read group set.
|
|
*/
|
|
readGroupSetId: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Operation>;
|
|
/**
|
|
* Gets a read group set by ID.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** The ID of the read group set. */
|
|
readGroupSetId: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<ReadGroupSet>;
|
|
/**
|
|
* Creates read group sets by asynchronously importing the provided
|
|
* information.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* The caller must have WRITE permissions to the dataset.
|
|
*
|
|
* ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
|
|
*
|
|
* - Tags will be converted to strings - tag types are not preserved
|
|
* - Comments (`@CO`) in the input file header will not be preserved
|
|
* - Original header order of references (`@SQ`) will not be preserved
|
|
* - Any reverse stranded unmapped reads will be reverse complemented, and
|
|
* their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
|
|
* - Unmapped reads will be stripped of positional information (reference name
|
|
* and position)
|
|
*/
|
|
import(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Operation>;
|
|
/**
|
|
* Updates a read group set.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* This method supports patch semantics.
|
|
*/
|
|
patch(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* The ID of the read group set to be updated. The caller must have WRITE
|
|
* permissions to the dataset associated with this read group set.
|
|
*/
|
|
readGroupSetId: string;
|
|
/**
|
|
* An optional mask specifying which fields to update. Supported fields:
|
|
*
|
|
* * name.
|
|
* * referenceSetId.
|
|
*
|
|
* Leaving `updateMask` unset is equivalent to specifying all mutable
|
|
* fields.
|
|
*/
|
|
updateMask?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<ReadGroupSet>;
|
|
/**
|
|
* Searches for read group sets matching the criteria.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchReadGroupSetsResponse>;
|
|
coveragebuckets: CoveragebucketsResource;
|
|
}
|
|
interface ReadsResource {
|
|
/**
|
|
* Gets a list of reads for one or more read group sets.
|
|
*
|
|
* For the definitions of read group sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Reads search operates over a genomic coordinate space of reference sequence
|
|
* & position defined over the reference sequences to which the requested
|
|
* read group sets are aligned.
|
|
*
|
|
* If a target positional range is specified, search returns all reads whose
|
|
* alignment to the reference genome overlap the range. A query which
|
|
* specifies only read group set IDs yields all reads in those read group
|
|
* sets, including unmapped reads.
|
|
*
|
|
* All reads returned (including reads on subsequent pages) are ordered by
|
|
* genomic coordinate (by reference sequence, then position). Reads with
|
|
* equivalent genomic coordinates are returned in an unspecified order. This
|
|
* order is consistent, such that two queries for the same content (regardless
|
|
* of page size) yield reads in the same order across their respective streams
|
|
* of paginated responses.
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchReadsResponse>;
|
|
}
|
|
interface BasesResource {
|
|
/**
|
|
* Lists the bases in a reference, optionally restricted to a range.
|
|
*
|
|
* For the definitions of references and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
|
|
*/
|
|
list(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/**
|
|
* The end position (0-based, exclusive) of this query. Defaults to the length
|
|
* of this reference.
|
|
*/
|
|
end?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/**
|
|
* The maximum number of bases to return in a single page. If unspecified,
|
|
* defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
|
|
* pairs).
|
|
*/
|
|
pageSize?: number;
|
|
/**
|
|
* The continuation token, which is used to page through large result sets.
|
|
* To get the next page of results, set this parameter to the value of
|
|
* `nextPageToken` from the previous response.
|
|
*/
|
|
pageToken?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** The ID of the reference. */
|
|
referenceId: string;
|
|
/** The start position (0-based) of this query. Defaults to 0. */
|
|
start?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<ListBasesResponse>;
|
|
}
|
|
interface ReferencesResource {
|
|
/**
|
|
* Gets a reference.
|
|
*
|
|
* For the definitions of references and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** The ID of the reference. */
|
|
referenceId: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Reference>;
|
|
/**
|
|
* Searches for references which match the given criteria.
|
|
*
|
|
* For the definitions of references and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchReferencesResponse>;
|
|
bases: BasesResource;
|
|
}
|
|
interface ReferencesetsResource {
|
|
/**
|
|
* Gets a reference set.
|
|
*
|
|
* For the definitions of references and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** The ID of the reference set. */
|
|
referenceSetId: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<ReferenceSet>;
|
|
/**
|
|
* Searches for reference sets which match the given criteria.
|
|
*
|
|
* For the definitions of references and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchReferenceSetsResponse>;
|
|
}
|
|
interface VariantsResource {
|
|
/**
|
|
* Creates a new variant.
|
|
*
|
|
* For the definitions of variants and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
create(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Variant>;
|
|
/**
|
|
* Deletes a variant.
|
|
*
|
|
* For the definitions of variants and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
delete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
/** The ID of the variant to be deleted. */
|
|
variantId: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Gets a variant by ID.
|
|
*
|
|
* For the definitions of variants and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
/** The ID of the variant. */
|
|
variantId: string;
|
|
}): Request<Variant>;
|
|
/**
|
|
* Creates variant data by asynchronously importing the provided information.
|
|
*
|
|
* For the definitions of variant sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* The variants for import will be merged with any existing variant that
|
|
* matches its reference sequence, start, end, reference bases, and
|
|
* alternative bases. If no such variant exists, a new one will be created.
|
|
*
|
|
* When variants are merged, the call information from the new variant
|
|
* is added to the existing variant, and Variant info fields are merged
|
|
* as specified in
|
|
* infoMergeConfig.
|
|
* As a special case, for single-sample VCF files, QUAL and FILTER fields will
|
|
* be moved to the call level; these are sometimes interpreted in a
|
|
* call-specific context.
|
|
* Imported VCF headers are appended to the metadata already in a variant set.
|
|
*/
|
|
import(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<Operation>;
|
|
/**
|
|
* Merges the given variants with existing variants.
|
|
*
|
|
* For the definitions of variants and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Each variant will be
|
|
* merged with an existing variant that matches its reference sequence,
|
|
* start, end, reference bases, and alternative bases. If no such variant
|
|
* exists, a new one will be created.
|
|
*
|
|
* When variants are merged, the call information from the new variant
|
|
* is added to the existing variant. Variant info fields are merged as
|
|
* specified in the
|
|
* infoMergeConfig
|
|
* field of the MergeVariantsRequest.
|
|
*
|
|
* Please exercise caution when using this method! It is easy to introduce
|
|
* mistakes in existing variants and difficult to back out of them. For
|
|
* example,
|
|
* suppose you were trying to merge a new variant with an existing one and
|
|
* both
|
|
* variants contain calls that belong to callsets with the same callset ID.
|
|
*
|
|
* // Existing variant - irrelevant fields trimmed for clarity
|
|
* {
|
|
* "variantSetId": "10473108253681171589",
|
|
* "referenceName": "1",
|
|
* "start": "10582",
|
|
* "referenceBases": "G",
|
|
* "alternateBases": [
|
|
* "A"
|
|
* ],
|
|
* "calls": [
|
|
* {
|
|
* "callSetId": "10473108253681171589-0",
|
|
* "callSetName": "CALLSET0",
|
|
* "genotype": [
|
|
* 0,
|
|
* 1
|
|
* ],
|
|
* }
|
|
* ]
|
|
* }
|
|
*
|
|
* // New variant with conflicting call information
|
|
* {
|
|
* "variantSetId": "10473108253681171589",
|
|
* "referenceName": "1",
|
|
* "start": "10582",
|
|
* "referenceBases": "G",
|
|
* "alternateBases": [
|
|
* "A"
|
|
* ],
|
|
* "calls": [
|
|
* {
|
|
* "callSetId": "10473108253681171589-0",
|
|
* "callSetName": "CALLSET0",
|
|
* "genotype": [
|
|
* 1,
|
|
* 1
|
|
* ],
|
|
* }
|
|
* ]
|
|
* }
|
|
*
|
|
* The resulting merged variant would overwrite the existing calls with those
|
|
* from the new variant:
|
|
*
|
|
* {
|
|
* "variantSetId": "10473108253681171589",
|
|
* "referenceName": "1",
|
|
* "start": "10582",
|
|
* "referenceBases": "G",
|
|
* "alternateBases": [
|
|
* "A"
|
|
* ],
|
|
* "calls": [
|
|
* {
|
|
* "callSetId": "10473108253681171589-0",
|
|
* "callSetName": "CALLSET0",
|
|
* "genotype": [
|
|
* 1,
|
|
* 1
|
|
* ],
|
|
* }
|
|
* ]
|
|
* }
|
|
*
|
|
* This may be the desired outcome, but it is up to the user to determine if
|
|
* if that is indeed the case.
|
|
*/
|
|
merge(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Updates a variant.
|
|
*
|
|
* For the definitions of variants and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* This method supports patch semantics. Returns the modified variant without
|
|
* its calls.
|
|
*/
|
|
patch(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* An optional mask specifying which fields to update. At this time, mutable
|
|
* fields are names and
|
|
* info. Acceptable values are "names" and
|
|
* "info". If unspecified, all mutable fields will be updated.
|
|
*/
|
|
updateMask?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
/** The ID of the variant to be updated. */
|
|
variantId: string;
|
|
}): Request<Variant>;
|
|
/**
|
|
* Gets a list of variants matching the criteria.
|
|
*
|
|
* For the definitions of variants and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchVariantsResponse>;
|
|
}
|
|
interface VariantsetsResource {
|
|
/**
|
|
* Creates a new variant set.
|
|
*
|
|
* For the definitions of variant sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* The provided variant set must have a valid `datasetId` set - all other
|
|
* fields are optional. Note that the `id` field will be ignored, as this is
|
|
* assigned by the server.
|
|
*/
|
|
create(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<VariantSet>;
|
|
/**
|
|
* Deletes a variant set including all variants, call sets, and calls within.
|
|
* This is not reversible.
|
|
*
|
|
* For the definitions of variant sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
delete(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
/** The ID of the variant set to be deleted. */
|
|
variantSetId: string;
|
|
}): Request<{}>;
|
|
/**
|
|
* Exports variant set data to an external destination.
|
|
*
|
|
* For the definitions of variant sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
export(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
/**
|
|
* Required. The ID of the variant set that contains variant data which
|
|
* should be exported. The caller must have READ access to this variant set.
|
|
*/
|
|
variantSetId: string;
|
|
}): Request<Operation>;
|
|
/**
|
|
* Gets a variant set by ID.
|
|
*
|
|
* For the definitions of variant sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
get(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
/** Required. The ID of the variant set. */
|
|
variantSetId: string;
|
|
}): Request<VariantSet>;
|
|
/**
|
|
* Updates a variant set using patch semantics.
|
|
*
|
|
* For the definitions of variant sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*/
|
|
patch(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/**
|
|
* An optional mask specifying which fields to update. Supported fields:
|
|
*
|
|
* * metadata.
|
|
* * name.
|
|
* * description.
|
|
*
|
|
* Leaving `updateMask` unset is equivalent to specifying all mutable
|
|
* fields.
|
|
*/
|
|
updateMask?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
/** The ID of the variant to be updated (must already exist). */
|
|
variantSetId: string;
|
|
}): Request<VariantSet>;
|
|
/**
|
|
* Returns a list of all variant sets matching search criteria.
|
|
*
|
|
* For the definitions of variant sets and other genomics resources, see
|
|
* [Fundamentals of Google
|
|
* Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
*
|
|
* Implements
|
|
* [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
|
|
*/
|
|
search(request: {
|
|
/** V1 error format. */
|
|
"$.xgafv"?: string;
|
|
/** OAuth access token. */
|
|
access_token?: string;
|
|
/** Data format for response. */
|
|
alt?: string;
|
|
/** OAuth bearer token. */
|
|
bearer_token?: string;
|
|
/** JSONP */
|
|
callback?: string;
|
|
/** Selector specifying which fields to include in a partial response. */
|
|
fields?: string;
|
|
/** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */
|
|
key?: string;
|
|
/** OAuth 2.0 token for the current user. */
|
|
oauth_token?: string;
|
|
/** Pretty-print response. */
|
|
pp?: boolean;
|
|
/** Returns response with indentations and line breaks. */
|
|
prettyPrint?: boolean;
|
|
/** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */
|
|
quotaUser?: string;
|
|
/** Legacy upload protocol for media (e.g. "media", "multipart"). */
|
|
uploadType?: string;
|
|
/** Upload protocol for media (e.g. "raw", "multipart"). */
|
|
upload_protocol?: string;
|
|
}): Request<SearchVariantSetsResponse>;
|
|
}
|
|
}
|
|
}
|