// Type definitions for non-npm package Google Genomics API v1 1.0 // Project: https://cloud.google.com/genomics // Definitions by: Bolisov Alexey // Definitions: https://github.com/DefinitelyTyped/DefinitelyTyped // TypeScript Version: 2.3 // IMPORTANT // This file was generated by https://github.com/Bolisov/google-api-typings-generator. Please do not edit it manually. // In case of any problems please post issue to https://github.com/Bolisov/google-api-typings-generator // Generated from: https://genomics.googleapis.com/$discovery/rest?version=v1 /// declare namespace gapi.client { /** Load Genomics API v1 */ function load(name: "genomics", version: "v1"): PromiseLike; function load(name: "genomics", version: "v1", callback: () => any): void; const annotations: genomics.AnnotationsResource; const annotationsets: genomics.AnnotationsetsResource; const callsets: genomics.CallsetsResource; const datasets: genomics.DatasetsResource; const operations: genomics.OperationsResource; const readgroupsets: genomics.ReadgroupsetsResource; const reads: genomics.ReadsResource; const references: genomics.ReferencesResource; const referencesets: genomics.ReferencesetsResource; const variants: genomics.VariantsResource; const variantsets: genomics.VariantsetsResource; namespace genomics { interface Annotation { /** The annotation set to which this annotation belongs. */ annotationSetId?: string; /** The end position of the range on the reference, 0-based exclusive. */ end?: string; /** The server-generated annotation ID, unique across all annotations. */ id?: string; /** * A map of additional read alignment information. This must be of the form * map (string key mapping to a list of string values). */ info?: Record; /** The display name of this annotation. */ name?: string; /** The ID of the Google Genomics reference associated with this range. */ referenceId?: string; /** * The display name corresponding to the reference specified by * `referenceId`, for example `chr1`, `1`, or `chrX`. */ referenceName?: string; /** * Whether this range refers to the reverse strand, as opposed to the forward * strand. Note that regardless of this field, the start/end position of the * range always refer to the forward strand. */ reverseStrand?: boolean; /** The start position of the range on the reference, 0-based inclusive. */ start?: string; /** * A transcript value represents the assertion that a particular region of * the reference genome may be transcribed as RNA. An alternative splicing * pattern would be represented as a separate transcript object. This field * is only set for annotations of type `TRANSCRIPT`. */ transcript?: Transcript; /** * The data type for this annotation. Must match the containing annotation * set's type. */ type?: string; /** * A variant annotation, which describes the effect of a variant on the * genome, the coding sequence, and/or higher level consequences at the * organism level e.g. pathogenicity. This field is only set for annotations * of type `VARIANT`. */ variant?: VariantAnnotation; } interface AnnotationSet { /** The dataset to which this annotation set belongs. */ datasetId?: string; /** The server-generated annotation set ID, unique across all annotation sets. */ id?: string; /** * A map of additional read alignment information. This must be of the form * map (string key mapping to a list of string values). */ info?: Record; /** The display name for this annotation set. */ name?: string; /** * The ID of the reference set that defines the coordinate space for this * set's annotations. */ referenceSetId?: string; /** * The source URI describing the file from which this annotation set was * generated, if any. */ sourceUri?: string; /** The type of annotations contained within this set. */ type?: string; } interface BatchCreateAnnotationsRequest { /** * The annotations to be created. At most 4096 can be specified in a single * request. */ annotations?: Annotation[]; /** * A unique request ID which enables the server to detect duplicated requests. * If provided, duplicated requests will result in the same response; if not * provided, duplicated requests may result in duplicated data. For a given * annotation set, callers should not reuse `request_id`s when writing * different batches of annotations - behavior in this case is undefined. * A common approach is to use a UUID. For batch jobs where worker crashes are * a possibility, consider using some unique variant of a worker or run ID. */ requestId?: string; } interface BatchCreateAnnotationsResponse { /** * The resulting per-annotation entries, ordered consistently with the * original request. */ entries?: Entry[]; } interface Binding { /** * Specifies the identities requesting access for a Cloud Platform resource. * `members` can have the following values: * * * `allUsers`: A special identifier that represents anyone who is * on the internet; with or without a Google account. * * * `allAuthenticatedUsers`: A special identifier that represents anyone * who is authenticated with a Google account or a service account. * * * `user:{emailid}`: An email address that represents a specific Google * account. For example, `alice@gmail.com` or `joe@example.com`. * * * * `serviceAccount:{emailid}`: An email address that represents a service * account. For example, `my-other-app@appspot.gserviceaccount.com`. * * * `group:{emailid}`: An email address that represents a Google group. * For example, `admins@example.com`. * * * * `domain:{domain}`: A Google Apps domain name that represents all the * users of that domain. For example, `google.com` or `example.com`. */ members?: string[]; /** * Role that is assigned to `members`. * For example, `roles/viewer`, `roles/editor`, or `roles/owner`. * Required */ role?: string; } interface CallSet { /** The date this call set was created in milliseconds from the epoch. */ created?: string; /** The server-generated call set ID, unique across all call sets. */ id?: string; /** * A map of additional call set information. This must be of the form * map (string key mapping to a list of string values). */ info?: Record; /** The call set name. */ name?: string; /** The sample ID this call set corresponds to. */ sampleId?: string; /** * The IDs of the variant sets this call set belongs to. This field must * have exactly length one, as a call set belongs to a single variant set. * This field is repeated for compatibility with the * [GA4GH 0.5.1 * API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76). */ variantSetIds?: string[]; } interface CigarUnit { operation?: string; /** The number of genomic bases that the operation runs for. Required. */ operationLength?: string; /** * `referenceSequence` is only used at mismatches * (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). * Filling this field replaces SAM's MD tag. If the relevant information is * not available, this field is unset. */ referenceSequence?: string; } interface ClinicalCondition { /** * The MedGen concept id associated with this gene. * Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ */ conceptId?: string; /** The set of external IDs for this condition. */ externalIds?: ExternalId[]; /** A set of names for the condition. */ names?: string[]; /** * The OMIM id for this condition. * Search for these IDs at http://omim.org/ */ omimId?: string; } interface CodingSequence { /** * The end of the coding sequence on this annotation's reference sequence, * 0-based exclusive. Note that this position is relative to the reference * start, and *not* the containing annotation start. */ end?: string; /** * The start of the coding sequence on this annotation's reference sequence, * 0-based inclusive. Note that this position is relative to the reference * start, and *not* the containing annotation start. */ start?: string; } interface ComputeEngine { /** The names of the disks that were created for this pipeline. */ diskNames?: string[]; /** The instance on which the operation is running. */ instanceName?: string; /** The machine type of the instance. */ machineType?: string; /** The availability zone in which the instance resides. */ zone?: string; } interface CoverageBucket { /** * The average number of reads which are aligned to each individual * reference base in this bucket. */ meanCoverage?: number; /** The genomic coordinate range spanned by this bucket. */ range?: Range; } interface Dataset { /** The time this dataset was created, in seconds from the epoch. */ createTime?: string; /** The server-generated dataset ID, unique across all datasets. */ id?: string; /** The dataset name. */ name?: string; /** The Google Cloud project ID that this dataset belongs to. */ projectId?: string; } interface Entry { /** The created annotation, if creation was successful. */ annotation?: Annotation; /** The creation status. */ status?: Status; } interface Exon { /** * The end position of the exon on this annotation's reference sequence, * 0-based exclusive. Note that this is relative to the reference start, and * *not* the containing annotation start. */ end?: string; /** * The frame of this exon. Contains a value of 0, 1, or 2, which indicates * the offset of the first coding base of the exon within the reading frame * of the coding DNA sequence, if any. This field is dependent on the * strandedness of this annotation (see * Annotation.reverse_strand). * For forward stranded annotations, this offset is relative to the * exon.start. For reverse * strand annotations, this offset is relative to the * exon.end `- 1`. * * Unset if this exon does not intersect the coding sequence. Upon creation * of a transcript, the frame must be populated for all or none of the * coding exons. */ frame?: number; /** * The start position of the exon on this annotation's reference sequence, * 0-based inclusive. Note that this is relative to the reference start, and * **not** the containing annotation start. */ start?: string; } interface Experiment { /** * The instrument model used as part of this experiment. This maps to * sequencing technology in the SAM spec. */ instrumentModel?: string; /** * A client-supplied library identifier; a library is a collection of DNA * fragments which have been prepared for sequencing from a sample. This * field is important for quality control as error or bias can be introduced * during sample preparation. */ libraryId?: string; /** * The platform unit used as part of this experiment, for example * flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the * @RG PU field in the SAM spec. */ platformUnit?: string; /** The sequencing center used as part of this experiment. */ sequencingCenter?: string; } interface ExportReadGroupSetRequest { /** * Required. A Google Cloud Storage URI for the exported BAM file. * The currently authenticated user must have write access to the new file. * An error will be returned if the URI already contains data. */ exportUri?: string; /** * Required. The Google Cloud project ID that owns this * export. The caller must have WRITE access to this project. */ projectId?: string; /** * The reference names to export. If this is not specified, all reference * sequences, including unmapped reads, are exported. * Use `*` to export only unmapped reads. */ referenceNames?: string[]; } interface ExportVariantSetRequest { /** * Required. The BigQuery dataset to export data to. This dataset must already * exist. Note that this is distinct from the Genomics concept of "dataset". */ bigqueryDataset?: string; /** * Required. The BigQuery table to export data to. * If the table doesn't exist, it will be created. If it already exists, it * will be overwritten. */ bigqueryTable?: string; /** * If provided, only variant call information from the specified call sets * will be exported. By default all variant calls are exported. */ callSetIds?: string[]; /** The format for the exported data. */ format?: string; /** * Required. The Google Cloud project ID that owns the destination * BigQuery dataset. The caller must have WRITE access to this project. This * project will also own the resulting export job. */ projectId?: string; } interface ExternalId { /** The id used by the source of this data. */ id?: string; /** The name of the source of this data. */ sourceName?: string; } interface ImportReadGroupSetsRequest { /** * Required. The ID of the dataset these read group sets will belong to. The * caller must have WRITE permissions to this dataset. */ datasetId?: string; /** * The partition strategy describes how read groups are partitioned into read * group sets. */ partitionStrategy?: string; /** * The reference set to which the imported read group sets are aligned to, if * any. The reference names of this reference set must be a superset of those * found in the imported file headers. If no reference set id is provided, a * best effort is made to associate with a matching reference set. */ referenceSetId?: string; /** * A list of URIs pointing at [BAM * files](https://samtools.github.io/hts-specs/SAMv1.pdf) * in Google Cloud Storage. * Those URIs can include wildcards (*), but do not add or remove * matching files before import has completed. * * Note that Google Cloud Storage object listing is only eventually * consistent: files added may be not be immediately visible to * everyone. Thus, if using a wildcard it is preferable not to start * the import immediately after the files are created. */ sourceUris?: string[]; } interface ImportReadGroupSetsResponse { /** IDs of the read group sets that were created. */ readGroupSetIds?: string[]; } interface ImportVariantsRequest { /** * The format of the variant data being imported. If unspecified, defaults to * to `VCF`. */ format?: string; /** * A mapping between info field keys and the InfoMergeOperations to * be performed on them. This is plumbed down to the MergeVariantRequests * generated by the resulting import job. */ infoMergeConfig?: Record; /** * Convert reference names to the canonical representation. * hg19 haploytypes (those reference names containing "_hap") * are not modified in any way. * All other reference names are modified according to the following rules: * The reference name is capitalized. * The "chr" prefix is dropped for all autosomes and sex chromsomes. * For example "chr17" becomes "17" and "chrX" becomes "X". * All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT". */ normalizeReferenceNames?: boolean; /** * A list of URIs referencing variant files in Google Cloud Storage. URIs can * include wildcards [as described * here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames). * Note that recursive wildcards ('**') are not supported. */ sourceUris?: string[]; /** Required. The variant set to which variant data should be imported. */ variantSetId?: string; } interface ImportVariantsResponse { /** IDs of the call sets created during the import. */ callSetIds?: string[]; } interface LinearAlignment { /** * Represents the local alignment of this sequence (alignment matches, indels, * etc) against the reference. */ cigar?: CigarUnit[]; /** * The mapping quality of this alignment. Represents how likely * the read maps to this position as opposed to other locations. * * Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to * the nearest integer. */ mappingQuality?: number; /** The position of this alignment. */ position?: Position; } interface ListBasesResponse { /** * 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 offset position (0-based) of the given `sequence` from the * start of this `Reference`. This value will differ for each page * in a paginated request. */ offset?: string; /** A substring of the bases that make up this reference. */ sequence?: string; } interface ListCoverageBucketsResponse { /** * The length of each coverage bucket in base pairs. Note that buckets at the * end of a reference sequence may be shorter. This value is omitted if the * bucket width is infinity (the default behaviour, with no range or * `targetBucketWidth`). */ bucketWidth?: string; /** * The coverage buckets. The list of buckets is sparse; a bucket with 0 * overlapping reads is not returned. A bucket never crosses more than one * reference sequence. Each bucket has width `bucketWidth`, unless * its end is the end of the reference sequence. */ coverageBuckets?: CoverageBucket[]; /** * 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 ListDatasetsResponse { /** The list of matching Datasets. */ datasets?: Dataset[]; /** * 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 ListOperationsResponse { /** The standard List next-page token. */ 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; /** 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; /** * 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; } 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; /** 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; /** Runtime metadata on this Operation. */ runtimeMetadata?: Record; /** 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 key mapping to a list of string values). */ info?: Record; /** * 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 key mapping to a list of string values). */ info?: Record; /** 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; /** * 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>; /** * 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 exons 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 key mapping to a list of string values). */ info?: Record; /** 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 key mapping to a list of string values). */ info?: Record; /** * 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 key mapping to a list of string values). */ info?: Record; /** 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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Deletes an annotation. Caller must have WRITE permission for * the associated annotation set. */ delete(request: { /** V1 error format. */ "$.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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** The ID of the annotation to be retrieved. */ annotationId: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Searches for annotations that match the given criteria. Results are * ordered by genomic coordinate (by reference sequence, then position). * Annotations with equivalent genomic coordinates are returned in an * unspecified order. This order is consistent, such that two queries for the * same content (regardless of page size) yield annotations in the same order * across their respective streams of paginated responses. Caller must have * READ permission for the queried annotation sets. */ search(request: { /** V1 error format. */ "$.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; /** * Updates an annotation. Caller must have * WRITE permission for the associated dataset. */ update(request: { /** V1 error format. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** The ID of the annotation to be updated. */ annotationId: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** * An optional mask specifying which fields to update. Mutable fields are * name, * variant, * transcript, and * info. If unspecified, all mutable * fields will be updated. */ updateMask?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; } interface AnnotationsetsResource { /** * Creates a new annotation set. Caller must have WRITE permission for the * associated dataset. * * The following fields are required: * * * datasetId * * referenceSetId * * All other fields may be optionally specified, unless documented as being * server-generated (for example, the `id` field). */ create(request: { /** V1 error format. */ "$.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; /** * 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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Updates an annotation set. The update must respect all mutability * restrictions and other invariants described on the annotation set resource. * Caller must have WRITE permission for the associated dataset. */ update(request: { /** V1 error format. */ "$.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; } 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Deletes a call set. * * For the definitions of call sets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) */ delete(request: { /** V1 error format. */ "$.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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** The ID of the call set. */ callSetId: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Updates a call set. * * For the definitions of call sets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * This method supports patch semantics. */ patch(request: { /** V1 error format. */ "$.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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; } interface DatasetsResource { /** * Creates a new dataset. * * For the definitions of datasets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) */ create(request: { /** V1 error format. */ "$.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; /** * 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; /** * Gets the access control policy for the dataset. This is empty if the * policy or resource does not exist. * * See Getting a * Policy 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** * REQUIRED: The resource for which policy is being specified. Format is * `datasets/`. */ resource: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Lists datasets within a project. * * For the definitions of datasets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) */ list(request: { /** V1 error format. */ "$.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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** The ID of the dataset to be updated. */ datasetId: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** * An optional mask specifying which fields to update. At this time, the only * mutable field is name. The only * acceptable value is "name". If unspecified, all mutable fields will be * updated. */ updateMask?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Sets the access control policy on the specified dataset. Replaces any * existing policy. * * For the definitions of datasets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * See Setting a * Policy for more information. */ setIamPolicy(request: { /** V1 error format. */ "$.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/`. */ 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; /** * Returns permissions that a caller has on the specified resource. * See Testing * Permissions 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** * REQUIRED: The resource for which policy is being specified. Format is * `datasets/`. */ resource: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Undeletes a dataset by restoring a dataset which was deleted via this API. * * For the definitions of datasets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * This operation is only possible for a week after the deletion occurred. */ undelete(request: { /** V1 error format. */ "$.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; } 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; /** 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; } 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; } 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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** The ID of the read group set. */ readGroupSetId: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Creates read group sets by asynchronously importing the provided * information. * * For the definitions of read group sets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * The caller must have WRITE permissions to the dataset. * * ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import * * - Tags will be converted to strings - tag types are not preserved * - Comments (`@CO`) in the input file header will not be preserved * - Original header order of references (`@SQ`) will not be preserved * - Any reverse stranded unmapped reads will be reverse complemented, and * their qualities (also the "BQ" and "OQ" tags, if any) will be reversed * - Unmapped reads will be stripped of positional information (reference name * and position) */ import(request: { /** V1 error format. */ "$.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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** * The ID of the read group set to be updated. The caller must have WRITE * permissions to the dataset associated with this read group set. */ readGroupSetId: string; /** * An optional mask specifying which fields to update. Supported fields: * * * name. * * referenceSetId. * * Leaving `updateMask` unset is equivalent to specifying all mutable * fields. */ updateMask?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Searches for read group sets matching the criteria. * * For the definitions of read group sets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * Implements * [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). */ search(request: { /** V1 error format. */ "$.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; 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; } interface BasesResource { /** * Lists the bases in a reference, optionally restricted to a range. * * For the definitions of references and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * Implements * [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221). */ list(request: { /** V1 error format. */ "$.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; } 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** The ID of the reference. */ referenceId: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Searches for references which match the given criteria. * * For the definitions of references and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * Implements * [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146). */ search(request: { /** V1 error format. */ "$.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; 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** The ID of the reference set. */ referenceSetId: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Searches for reference sets which match the given criteria. * * For the definitions of references and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * Implements * [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71) */ search(request: { /** V1 error format. */ "$.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; } 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; /** * Deletes a variant. * * For the definitions of variants and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) */ delete(request: { /** V1 error format. */ "$.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; /** * 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; /** * 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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; }): Request; } interface VariantsetsResource { /** * Creates a new variant set. * * For the definitions of variant sets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) * * The provided variant set must have a valid `datasetId` set - all other * fields are optional. Note that the `id` field will be ignored, as this is * assigned by the server. */ create(request: { /** V1 error format. */ "$.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; /** * 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; /** * 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. */ "$.xgafv"?: string; /** OAuth access token. */ access_token?: string; /** Data format for response. */ alt?: string; /** OAuth bearer token. */ bearer_token?: string; /** JSONP */ callback?: string; /** Selector specifying which fields to include in a partial response. */ fields?: string; /** API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token. */ key?: string; /** OAuth 2.0 token for the current user. */ oauth_token?: string; /** Pretty-print response. */ pp?: boolean; /** Returns response with indentations and line breaks. */ prettyPrint?: boolean; /** Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters. */ quotaUser?: string; /** Legacy upload protocol for media (e.g. "media", "multipart"). */ uploadType?: string; /** Upload protocol for media (e.g. "raw", "multipart"). */ upload_protocol?: string; /** Required. The ID of the variant set. */ variantSetId: string; }): Request; /** * Updates a variant set using patch semantics. * * For the definitions of variant sets and other genomics resources, see * [Fundamentals of Google * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) */ patch(request: { /** V1 error format. */ "$.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; /** * 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; } } }