genomics

package
v0.0.0-...-375ceb8 Latest Latest
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 Go to latest Published: Jul 31, 2015 License: BSD-3-Clause Imports: 11 Imported by: 0

Documentation

Overview

Package genomics provides access to the Genomics API.

Usage example: 

import "google.golang.org/api/genomics/v1"
...
genomicsService, err := genomics.New(oauthHttpClient)

Index

Constants

View Source 
const (
	// View and manage your data in Google BigQuery
	BigqueryScope = "https://www.googleapis.com/auth/bigquery"

	// View and manage your data across Google Cloud Platform services
	CloudPlatformScope = "https://www.googleapis.com/auth/cloud-platform"

	// Manage your data in Google Cloud Storage
	DevstorageReadWriteScope = "https://www.googleapis.com/auth/devstorage.read_write"

	// View and manage Genomics data
	GenomicsScope = "https://www.googleapis.com/auth/genomics"

	// View Genomics data
	GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics.readonly"
)

OAuth2 scopes used by this API.

Variables

This section is empty.

Functions

This section is empty.

Types

type CallSet 

type CallSet struct {
	// Created: The date this call set was created in milliseconds from the
	// epoch.
	Created int64 `json:"created,omitempty,string"`

	// Id: The server-generated call set ID, unique across all call sets.
	Id string `json:"id,omitempty"`

	// Info: A map of additional call set information. This must be of the
	// form map (string key mapping to a list of string values).
	Info *CallSetInfo `json:"info,omitempty"`

	// Name: The call set name.
	Name string `json:"name,omitempty"`

	// SampleId: The sample ID this call set corresponds to.
	SampleId string `json:"sampleId,omitempty"`

	// VariantSetIds: The IDs of the variant sets this call set belongs to.
	VariantSetIds []string `json:"variantSetIds,omitempty"`
}

CallSet: A call set is a collection of variant calls, typically for one sample. It belongs to a variant set.

type CallSetInfo 

type CallSetInfo struct {
}

CallSetInfo: A map of additional call set information. This must be of the form map (string key mapping to a list of string values).

type CallsetsCreateCall 

type CallsetsCreateCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsCreateCall) Do 

func (c *CallsetsCreateCall) Do() (*CallSet, error)

func (*CallsetsCreateCall) Fields 

func (c *CallsetsCreateCall) Fields(s ...googleapi.Field) *CallsetsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsDeleteCall 

type CallsetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsDeleteCall) Do 

func (c *CallsetsDeleteCall) Do() (*Empty, error)

func (*CallsetsDeleteCall) Fields 

func (c *CallsetsDeleteCall) Fields(s ...googleapi.Field) *CallsetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsGetCall 

type CallsetsGetCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsGetCall) Do 

func (c *CallsetsGetCall) Do() (*CallSet, error)

func (*CallsetsGetCall) Fields 

func (c *CallsetsGetCall) Fields(s ...googleapi.Field) *CallsetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsPatchCall 

type CallsetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsPatchCall) Do 

func (c *CallsetsPatchCall) Do() (*CallSet, error)

func (*CallsetsPatchCall) Fields 

func (c *CallsetsPatchCall) Fields(s ...googleapi.Field) *CallsetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*CallsetsPatchCall) UpdateMask 

func (c *CallsetsPatchCall) UpdateMask(updateMask string) *CallsetsPatchCall

UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. At this time, the only mutable field is [name][google.genomics.v1.CallSet.name]. The only acceptable value is "name". If unspecified, all mutable fields will be updated.

type CallsetsSearchCall 

type CallsetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*CallsetsSearchCall) Do 

func (c *CallsetsSearchCall) Do() (*SearchCallSetsResponse, error)

func (*CallsetsSearchCall) Fields 

func (c *CallsetsSearchCall) Fields(s ...googleapi.Field) *CallsetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type CallsetsService 

type CallsetsService struct {
	// contains filtered or unexported fields
}

func NewCallsetsService 

func NewCallsetsService(s *Service) *CallsetsService

func (*CallsetsService) Create 

func (r *CallsetsService) Create(callset *CallSet) *CallsetsCreateCall

Create: Creates a new call set.

func (*CallsetsService) Delete 

func (r *CallsetsService) Delete(callSetId string) *CallsetsDeleteCall

Delete: Deletes a call set.

func (*CallsetsService) Get 

func (r *CallsetsService) Get(callSetId string) *CallsetsGetCall

Get: Gets a call set by ID.

func (*CallsetsService) Patch 

func (r *CallsetsService) Patch(callSetId string, callset *CallSet) *CallsetsPatchCall

Patch: Updates a call set. This method supports patch semantics.

func (*CallsetsService) Search 

func (r *CallsetsService) Search(searchcallsetsrequest *SearchCallSetsRequest) *CallsetsSearchCall

Search: Gets a list of call sets matching the criteria. Implements [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/bl ob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).

type CancelOperationRequest 

type CancelOperationRequest struct {
}

CancelOperationRequest: The request message for [Operations.CancelOperation][google.longrunning.Operations.CancelOpera tion].

type CigarUnit 

type CigarUnit struct {
	// Possible values:
	//   "OPERATION_UNSPECIFIED"
	//   "ALIGNMENT_MATCH"
	//   "INSERT"
	//   "DELETE"
	//   "SKIP"
	//   "CLIP_SOFT"
	//   "CLIP_HARD"
	//   "PAD"
	//   "SEQUENCE_MATCH"
	//   "SEQUENCE_MISMATCH"
	Operation string `json:"operation,omitempty"`

	// OperationLength: The number of genomic bases that the operation runs
	// for. Required.
	OperationLength int64 `json:"operationLength,omitempty,string"`

	// ReferenceSequence: `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 `json:"referenceSequence,omitempty"`
}

CigarUnit: A single CIGAR operation.

type CoverageBucket 

type CoverageBucket struct {
	// MeanCoverage: The average number of reads which are aligned to each
	// individual reference base in this bucket.
	MeanCoverage float64 `json:"meanCoverage,omitempty"`

	// Range: The genomic coordinate range spanned by this bucket.
	Range *Range `json:"range,omitempty"`
}

CoverageBucket: A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.

type Dataset 

type Dataset struct {
	// CreateTime: The time this dataset was created, in seconds from the
	// epoch.
	CreateTime string `json:"createTime,omitempty"`

	// Id: The server-generated dataset ID, unique across all datasets.
	Id string `json:"id,omitempty"`

	// Name: The dataset name.
	Name string `json:"name,omitempty"`

	// ProjectId: The Google Developers Console project ID that this dataset
	// belongs to.
	ProjectId string `json:"projectId,omitempty"`
}

Dataset: A Dataset is a collection of genomic data.

type DatasetsCreateCall 

type DatasetsCreateCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsCreateCall) Do 

func (c *DatasetsCreateCall) Do() (*Dataset, error)

func (*DatasetsCreateCall) Fields 

func (c *DatasetsCreateCall) Fields(s ...googleapi.Field) *DatasetsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsDeleteCall 

type DatasetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsDeleteCall) Do 

func (c *DatasetsDeleteCall) Do() (*Empty, error)

func (*DatasetsDeleteCall) Fields 

func (c *DatasetsDeleteCall) Fields(s ...googleapi.Field) *DatasetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsGetCall 

type DatasetsGetCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsGetCall) Do 

func (c *DatasetsGetCall) Do() (*Dataset, error)

func (*DatasetsGetCall) Fields 

func (c *DatasetsGetCall) Fields(s ...googleapi.Field) *DatasetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type DatasetsListCall 

type DatasetsListCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsListCall) Do 

func (c *DatasetsListCall) Do() (*ListDatasetsResponse, error)

func (*DatasetsListCall) Fields 

func (c *DatasetsListCall) Fields(s ...googleapi.Field) *DatasetsListCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*DatasetsListCall) PageSize 

func (c *DatasetsListCall) PageSize(pageSize int64) *DatasetsListCall

PageSize sets the optional parameter "pageSize": The maximum number of results returned by this request. If unspecified, defaults to 50. The maximum value is 1024.

func (*DatasetsListCall) PageToken 

func (c *DatasetsListCall) PageToken(pageToken string) *DatasetsListCall

PageToken sets the optional parameter "pageToken": 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.

func (*DatasetsListCall) ProjectId 

func (c *DatasetsListCall) ProjectId(projectId string) *DatasetsListCall

ProjectId sets the optional parameter "projectId": Required. The project to list datasets for.

type DatasetsPatchCall 

type DatasetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsPatchCall) Do 

func (c *DatasetsPatchCall) Do() (*Dataset, error)

func (*DatasetsPatchCall) Fields 

func (c *DatasetsPatchCall) Fields(s ...googleapi.Field) *DatasetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*DatasetsPatchCall) UpdateMask 

func (c *DatasetsPatchCall) UpdateMask(updateMask string) *DatasetsPatchCall

UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. At this time, the only mutable field is [name][google.genomics.v1.Dataset.name]. The only acceptable value is "name". If unspecified, all mutable fields will be updated.

type DatasetsService 

type DatasetsService struct {
	// contains filtered or unexported fields
}

func NewDatasetsService 

func NewDatasetsService(s *Service) *DatasetsService

func (*DatasetsService) Create 

func (r *DatasetsService) Create(dataset *Dataset) *DatasetsCreateCall

Create: Creates a new dataset.

func (*DatasetsService) Delete 

func (r *DatasetsService) Delete(datasetId string) *DatasetsDeleteCall

Delete: Deletes a dataset.

func (*DatasetsService) Get 

func (r *DatasetsService) Get(datasetId string) *DatasetsGetCall

Get: Gets a dataset by ID.

func (*DatasetsService) List 

func (r *DatasetsService) List() *DatasetsListCall

List: Lists datasets within a project.

func (*DatasetsService) Patch 

func (r *DatasetsService) Patch(datasetId string, dataset *Dataset) *DatasetsPatchCall

Patch: Updates a dataset. This method supports patch semantics.

func (*DatasetsService) Undelete 

func (r *DatasetsService) Undelete(datasetId string, undeletedatasetrequest *UndeleteDatasetRequest) *DatasetsUndeleteCall

Undelete: Undeletes a dataset by restoring a dataset which was deleted via this API. This operation is only possible for a week after the deletion occurred.

type DatasetsUndeleteCall 

type DatasetsUndeleteCall struct {
	// contains filtered or unexported fields
}

func (*DatasetsUndeleteCall) Do 

func (c *DatasetsUndeleteCall) Do() (*Dataset, error)

func (*DatasetsUndeleteCall) Fields 

func (c *DatasetsUndeleteCall) Fields(s ...googleapi.Field) *DatasetsUndeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type Empty 

type Empty struct {
}

Empty: A generic empty message that you can re-use to avoid defining duplicated empty messages in your APIs. A typical example is to use it as the request or the response type of an API method. For instance: service Foo { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON representation for `Empty` is empty JSON object `{}`.

type Experiment 

type Experiment struct {
	// InstrumentModel: The instrument model used as part of this
	// experiment. This maps to sequencing technology in BAM.
	InstrumentModel string `json:"instrumentModel,omitempty"`

	// LibraryId: The library used as part of this experiment. Note: This is
	// not an actual ID within this repository, but rather an identifier for
	// a library which may be meaningful to some external system.
	LibraryId string `json:"libraryId,omitempty"`

	// PlatformUnit: The platform unit used as part of this experiment e.g.
	// flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to
	// the @RG PU field in the SAM spec.
	PlatformUnit string `json:"platformUnit,omitempty"`

	// SequencingCenter: The sequencing center used as part of this
	// experiment.
	SequencingCenter string `json:"sequencingCenter,omitempty"`
}

type ExportReadGroupSetRequest 

type ExportReadGroupSetRequest struct {
	// ExportUri: 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 `json:"exportUri,omitempty"`

	// ProjectId: Required. The Google Developers Console project ID that
	// owns this export.
	ProjectId string `json:"projectId,omitempty"`

	// ReferenceNames: 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 `json:"referenceNames,omitempty"`
}

ExportReadGroupSetRequest: The read group set export request.

type ExportVariantSetRequest 

type ExportVariantSetRequest struct {
	// BigqueryDataset: 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 `json:"bigqueryDataset,omitempty"`

	// BigqueryTable: 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 `json:"bigqueryTable,omitempty"`

	// CallSetIds: If provided, only variant call information from the
	// specified call sets will be exported. By default all variant calls
	// are exported.
	CallSetIds []string `json:"callSetIds,omitempty"`

	// Format: The format for the exported data.
	//
	// Possible values:
	//   "FORMAT_UNSPECIFIED"
	//   "FORMAT_BIGQUERY"
	Format string `json:"format,omitempty"`

	// ProjectId: 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 `json:"projectId,omitempty"`
}

ExportVariantSetRequest: The variant data export request.

type ImportReadGroupSetsRequest 

type ImportReadGroupSetsRequest struct {
	// DatasetId: Required. The ID of the dataset these read group sets will
	// belong to. The caller must have WRITE permissions to this dataset.
	DatasetId string `json:"datasetId,omitempty"`

	// PartitionStrategy: The partition strategy describes how read groups
	// are partitioned into read group sets.
	//
	// Possible values:
	//   "PARTITION_STRATEGY_UNSPECIFIED"
	//   "PER_FILE_PER_SAMPLE"
	//   "MERGE_ALL"
	PartitionStrategy string `json:"partitionStrategy,omitempty"`

	// ReferenceSetId: 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 `json:"referenceSetId,omitempty"`

	// SourceUris: A list of URIs pointing at BAM files in Google Cloud
	// Storage.
	SourceUris []string `json:"sourceUris,omitempty"`
}

ImportReadGroupSetsRequest: The read group set import request.

type ImportReadGroupSetsResponse 

type ImportReadGroupSetsResponse struct {
	// ReadGroupSetIds: IDs of the read group sets that were created.
	ReadGroupSetIds []string `json:"readGroupSetIds,omitempty"`
}

ImportReadGroupSetsResponse: The read group set import response.

type ImportVariantsRequest 

type ImportVariantsRequest struct {
	// Format: The format of the variant data being imported. If
	// unspecified, defaults to to `VCF`.
	//
	// Possible values:
	//   "FORMAT_UNSPECIFIED"
	//   "FORMAT_VCF"
	//   "FORMAT_COMPLETE_GENOMICS"
	Format string `json:"format,omitempty"`

	// NormalizeReferenceNames: 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 bool `json:"normalizeReferenceNames,omitempty"`

	// SourceUris: 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/WildcardNa
	// mes). Note that recursive wildcards ('**') are not supported.
	SourceUris []string `json:"sourceUris,omitempty"`

	// VariantSetId: Required. The variant set to which variant data should
	// be imported.
	VariantSetId string `json:"variantSetId,omitempty"`
}

ImportVariantsRequest: The variant data import request.

type ImportVariantsResponse 

type ImportVariantsResponse struct {
	// CallSetIds: IDs of the call sets that were created.
	CallSetIds []string `json:"callSetIds,omitempty"`
}

ImportVariantsResponse: The variant data import response.

type LinearAlignment 

type LinearAlignment struct {
	// Cigar: Represents the local alignment of this sequence (alignment
	// matches, indels, etc) against the reference.
	Cigar []*CigarUnit `json:"cigar,omitempty"`

	// MappingQuality: The mapping quality of this alignment. Represents how
	// likely the read maps to this position as opposed to other locations.
	MappingQuality int64 `json:"mappingQuality,omitempty"`

	// Position: The position of this alignment.
	Position *Position `json:"position,omitempty"`
}

LinearAlignment: A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.

type ListBasesResponse 

type ListBasesResponse struct {
	// NextPageToken: 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 `json:"nextPageToken,omitempty"`

	// Offset: 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 int64 `json:"offset,omitempty,string"`

	// Sequence: A substring of the bases that make up this reference.
	Sequence string `json:"sequence,omitempty"`
}

type ListCoverageBucketsResponse 

type ListCoverageBucketsResponse struct {
	// BucketWidth: 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 int64 `json:"bucketWidth,omitempty,string"`

	// CoverageBuckets: 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 `json:"coverageBuckets,omitempty"`

	// NextPageToken: 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 `json:"nextPageToken,omitempty"`
}

type ListDatasetsResponse 

type ListDatasetsResponse struct {
	// Datasets: The list of matching Datasets.
	Datasets []*Dataset `json:"datasets,omitempty"`

	// NextPageToken: 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 `json:"nextPageToken,omitempty"`
}

ListDatasetsResponse: The dataset list response.

type ListOperationsResponse 

type ListOperationsResponse struct {
	// NextPageToken: The standard List next-page token.
	NextPageToken string `json:"nextPageToken,omitempty"`

	// Operations: A list of operations that matches the specified filter in
	// the request.
	Operations []*Operation `json:"operations,omitempty"`
}

ListOperationsResponse: The response message for [Operations.ListOperations][google.longrunning.Operations.ListOperatio ns].

type MergeVariantsRequest 

type MergeVariantsRequest struct {
	// VariantSetId: The destination variant set.
	VariantSetId string `json:"variantSetId,omitempty"`

	// Variants: The variants to be merged with existing variants.
	Variants []*Variant `json:"variants,omitempty"`
}

type Operation 

type Operation struct {
	// Done: If the value is `false`, it means the operation is still in
	// progress. If true, the operation is completed and the `result` is
	// available.
	Done bool `json:"done,omitempty"`

	// Error: The error result of the operation in case of failure.
	Error *Status `json:"error,omitempty"`

	// Metadata: An
	// [OperationMetadata][google.genomics.v1.OperationMetadata] object.
	// This will always be returned with the
	// [Operation][google.longrunning.Operation].
	Metadata OperationMetadata `json:"metadata,omitempty"`

	// Name: The server-assigned name, which is only unique within the same
	// service that originally returns it. For example:
	// `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
	Name string `json:"name,omitempty"`

	// Response: If importing
	// [ReadGroupSets][google.genomics.v1.ReadGroupSet], an
	// [ImportReadGroupSetsResponse][google.genomics.v1.ImportReadGroupSetsRe
	// sponse] is returned. If importing
	// [Variants][google.genomics.v1.Variant], an
	// [ImportVariantsResponse][google.genomics.v1.ImportVariantsResponse]
	// is returned. For exports, an empty response is returned.
	Response OperationResponse `json:"response,omitempty"`
}

Operation: This resource represents a long-running operation that is the result of a network API call.

type OperationEvent 

type OperationEvent struct {
	// Description: Required description of event.
	Description string `json:"description,omitempty"`
}

OperationEvent: An event that occurred during an Operation[google.longrunning.Operation].

type OperationMetadata 

type OperationMetadata interface{}

type OperationMetadata1 

type OperationMetadata1 struct {
	// CreateTime: The time at which the job was submitted to the Genomics
	// service.
	CreateTime string `json:"createTime,omitempty"`

	// Events: 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 `json:"events,omitempty"`

	// ProjectId: The Google Cloud Project in which the job is scoped.
	ProjectId string `json:"projectId,omitempty"`

	// Request: 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 OperationMetadataRequest `json:"request,omitempty"`
}

OperationMetadata1: Metadata describing an Operation[google.longrunning.Operation].

type OperationMetadataRequest 

type OperationMetadataRequest interface{}

type OperationResponse 

type OperationResponse interface{}

type OperationsCancelCall 

type OperationsCancelCall struct {
	// contains filtered or unexported fields
}

func (*OperationsCancelCall) Do 

func (c *OperationsCancelCall) Do() (*Empty, error)

func (*OperationsCancelCall) Fields 

func (c *OperationsCancelCall) Fields(s ...googleapi.Field) *OperationsCancelCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type OperationsDeleteCall 

type OperationsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*OperationsDeleteCall) Do 

func (c *OperationsDeleteCall) Do() (*Empty, error)

func (*OperationsDeleteCall) Fields 

func (c *OperationsDeleteCall) Fields(s ...googleapi.Field) *OperationsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type OperationsGetCall 

type OperationsGetCall struct {
	// contains filtered or unexported fields
}

func (*OperationsGetCall) Do 

func (c *OperationsGetCall) Do() (*Operation, error)

func (*OperationsGetCall) Fields 

func (c *OperationsGetCall) Fields(s ...googleapi.Field) *OperationsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type OperationsListCall 

type OperationsListCall struct {
	// contains filtered or unexported fields
}

func (*OperationsListCall) Do 

func (c *OperationsListCall) Do() (*ListOperationsResponse, error)

func (*OperationsListCall) Fields 

func (c *OperationsListCall) Fields(s ...googleapi.Field) *OperationsListCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*OperationsListCall) Filter 

func (c *OperationsListCall) Filter(filter string) *OperationsListCall

Filter sets the optional parameter "filter": A string for filtering [Operations][google.longrunning.Operation]. The following filter fields are supported: * projectId: Required. Corresponds to [OperationMetadata.projectId][google.genomics.v1.OperationMetadata.pro ject_id]. * createTime: The time this job was created, in seconds from the [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `= 1432140000` * `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING`

func (*OperationsListCall) PageSize 

func (c *OperationsListCall) PageSize(pageSize int64) *OperationsListCall

PageSize sets the optional parameter "pageSize": The maximum number of results to return. If unspecified, defaults to 256. The maximum value is 2048.

func (*OperationsListCall) PageToken 

func (c *OperationsListCall) PageToken(pageToken string) *OperationsListCall

PageToken sets the optional parameter "pageToken": The standard List page token.

type OperationsService 

type OperationsService struct {
	// contains filtered or unexported fields
}

func NewOperationsService 

func NewOperationsService(s *Service) *OperationsService

func (*OperationsService) Cancel 

func (r *OperationsService) Cancel(name string, canceloperationrequest *CancelOperationRequest) *OperationsCancelCall

Cancel: 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][google.longrunning.Operations.GetOperation] or [Operations.ListOperations][google.longrunning.Operations.ListOperatio ns] to check whether the cancellation succeeded or the operation completed despite cancellation.

func (*OperationsService) Delete 

func (r *OperationsService) Delete(name string) *OperationsDeleteCall

Delete: This method is not implemented. To cancel an operation, please use [Operations.CancelOperation][google.longrunning.Operations.CancelOpera tion].

func (*OperationsService) Get 

func (r *OperationsService) Get(name string) *OperationsGetCall

Get: 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.

func (*OperationsService) List 

func (r *OperationsService) List(name string) *OperationsListCall

List: Lists operations that match the specified filter in the request.

type Position 

type Position struct {
	// Position: The 0-based offset from the start of the forward strand for
	// that reference.
	Position int64 `json:"position,omitempty,string"`

	// ReferenceName: The name of the reference in whatever reference set is
	// being used.
	ReferenceName string `json:"referenceName,omitempty"`

	// ReverseStrand: Whether this position is on the reverse strand, as
	// opposed to the forward strand.
	ReverseStrand bool `json:"reverseStrand,omitempty"`
}

Position: An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand.

type Program 

type Program struct {
	// CommandLine: The command line used to run this program.
	CommandLine string `json:"commandLine,omitempty"`

	// Id: The user specified locally unique ID of the program. Used along
	// with `prevProgramId` to define an ordering between programs.
	Id string `json:"id,omitempty"`

	// Name: The name of the program.
	Name string `json:"name,omitempty"`

	// PrevProgramId: The ID of the program run before this one.
	PrevProgramId string `json:"prevProgramId,omitempty"`

	// Version: The version of the program run.
	Version string `json:"version,omitempty"`
}

type Range 

type Range struct {
	// End: The end position of the range on the reference, 0-based
	// exclusive.
	End int64 `json:"end,omitempty,string"`

	// ReferenceName: The reference sequence name, for example `chr1`, `1`,
	// or `chrX`.
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The start position of the range on the reference, 0-based
	// inclusive.
	Start int64 `json:"start,omitempty,string"`
}

Range: A 0-based half-open genomic coordinate range for search requests.

type Read 

type Read struct {
	// AlignedQuality: The quality of the read sequence contained in this
	// alignment record. `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 []int64 `json:"alignedQuality,omitempty"`

	// AlignedSequence: The bases of the read sequence contained in this
	// alignment record, *without CIGAR operations applied*.
	// `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 `json:"alignedSequence,omitempty"`

	// Alignment: The linear alignment for this alignment record. This field
	// will be null if the read is unmapped.
	Alignment *LinearAlignment `json:"alignment,omitempty"`

	// DuplicateFragment: The fragment is a PCR or optical duplicate (SAM
	// flag 0x400)
	DuplicateFragment bool `json:"duplicateFragment,omitempty"`

	// FailedVendorQualityChecks: SAM flag 0x200
	FailedVendorQualityChecks bool `json:"failedVendorQualityChecks,omitempty"`

	// FragmentLength: The observed length of the fragment, equivalent to
	// TLEN in SAM.
	FragmentLength int64 `json:"fragmentLength,omitempty"`

	// FragmentName: The fragment name. Equivalent to QNAME (query template
	// name) in SAM.
	FragmentName string `json:"fragmentName,omitempty"`

	// Id: The server-generated read ID, unique across all reads. This is
	// different from the `fragmentName`.
	Id string `json:"id,omitempty"`

	// Info: A map of additional read alignment information. This must be of
	// the form map (string key mapping to a list of string values).
	Info *ReadInfo `json:"info,omitempty"`

	// NextMatePosition: 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 `json:"nextMatePosition,omitempty"`

	// NumberReads: The number of reads in the fragment (extension to SAM
	// flag 0x1).
	NumberReads int64 `json:"numberReads,omitempty"`

	// ProperPlacement: The orientation and the distance between reads from
	// the fragment are consistent with the sequencing protocol (SAM flag
	// 0x2)
	ProperPlacement bool `json:"properPlacement,omitempty"`

	// ReadGroupId: The ID of the read group this read belongs to. (Every
	// read must belong to exactly one read group.)
	ReadGroupId string `json:"readGroupId,omitempty"`

	// ReadGroupSetId: The ID of the read group set this read belongs to.
	// (Every read must belong to exactly one read group set.)
	ReadGroupSetId string `json:"readGroupSetId,omitempty"`

	// ReadNumber: The read number in sequencing. 0-based and less than
	// numberReads. This field replaces SAM flag 0x40 and 0x80.
	ReadNumber int64 `json:"readNumber,omitempty"`

	// SecondaryAlignment: 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 bool `json:"secondaryAlignment,omitempty"`

	// SupplementaryAlignment: 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 bool `json:"supplementaryAlignment,omitempty"`
}

Read: A read alignment describes a linear alignment of a string of DNA to a [reference sequence][google.genomics.v1.Reference], in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one [read group set][google.genomics.v1.ReadGroupSet]. ### Generating a reference-aligned sequence string When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } } return out ### Converting to SAM's CIGAR string The following pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr

type ReadGroup 

type ReadGroup struct {
	// DatasetId: The ID of the dataset this read group belongs to.
	DatasetId string `json:"datasetId,omitempty"`

	// Description: A free-form text description of this read group.
	Description string `json:"description,omitempty"`

	// Experiment: The experiment used to generate this read group.
	Experiment *Experiment `json:"experiment,omitempty"`

	// Id: 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 the `name` field.
	Id string `json:"id,omitempty"`

	// Info: A map of additional read group information. This must be of the
	// form map (string key mapping to a list of string values).
	Info *ReadGroupInfo `json:"info,omitempty"`

	// Name: The read group name. This corresponds to the @RG ID field in
	// the SAM spec.
	Name string `json:"name,omitempty"`

	// PredictedInsertSize: 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 int64 `json:"predictedInsertSize,omitempty"`

	// Programs: 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 `json:"programs,omitempty"`

	// ReferenceSetId: The reference set the reads in this read group are
	// aligned to. Required if there are any read alignments.
	ReferenceSetId string `json:"referenceSetId,omitempty"`

	// SampleId: The sample this read group's data was generated from. Note:
	// This is not an actual ID within this repository, but rather an
	// identifier for a sample which may be meaningful to some external
	// system.
	SampleId string `json:"sampleId,omitempty"`
}

ReadGroup: A read group is all the data that's processed the same way by the sequencer.

type ReadGroupInfo 

type ReadGroupInfo struct {
}

ReadGroupInfo: A map of additional read group information. This must be of the form map (string key mapping to a list of string values).

type ReadGroupSet 

type ReadGroupSet struct {
	// DatasetId: The dataset ID.
	DatasetId string `json:"datasetId,omitempty"`

	// Filename: The filename of the original source file for this read
	// group set, if any.
	Filename string `json:"filename,omitempty"`

	// Id: The server-generated read group set ID, unique for all read group
	// sets.
	Id string `json:"id,omitempty"`

	// Info: A map of additional read group set information.
	Info *ReadGroupSetInfo `json:"info,omitempty"`

	// Name: 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 `json:"name,omitempty"`

	// ReadGroups: The read groups in this set. There are typically 1-10
	// read groups in a read group set.
	ReadGroups []*ReadGroup `json:"readGroups,omitempty"`

	// ReferenceSetId: The reference set the reads in this read group set
	// are aligned to.
	ReferenceSetId string `json:"referenceSetId,omitempty"`
}

ReadGroupSet: A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way. * A read group set belongs to one dataset. * A read group belongs to one read group set. * A read belongs to one read group.

type ReadGroupSetInfo 

type ReadGroupSetInfo struct {
}

ReadGroupSetInfo: A map of additional read group set information.

type ReadInfo 

type ReadInfo struct {
}

ReadInfo: A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).

type ReadgroupsetsCoveragebucketsListCall 

type ReadgroupsetsCoveragebucketsListCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsCoveragebucketsListCall) Do 

func (c *ReadgroupsetsCoveragebucketsListCall) Do() (*ListCoverageBucketsResponse, error)

func (*ReadgroupsetsCoveragebucketsListCall) End 

func (c *ReadgroupsetsCoveragebucketsListCall) End(end int64) *ReadgroupsetsCoveragebucketsListCall

End sets the optional parameter "end": 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.

func (*ReadgroupsetsCoveragebucketsListCall) Fields 

func (c *ReadgroupsetsCoveragebucketsListCall) Fields(s ...googleapi.Field) *ReadgroupsetsCoveragebucketsListCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*ReadgroupsetsCoveragebucketsListCall) PageSize 

func (c *ReadgroupsetsCoveragebucketsListCall) PageSize(pageSize int64) *ReadgroupsetsCoveragebucketsListCall

PageSize sets the optional parameter "pageSize": The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 2048.

func (*ReadgroupsetsCoveragebucketsListCall) PageToken 

func (c *ReadgroupsetsCoveragebucketsListCall) PageToken(pageToken string) *ReadgroupsetsCoveragebucketsListCall

PageToken sets the optional parameter "pageToken": 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.

func (*ReadgroupsetsCoveragebucketsListCall) ReferenceName 

func (c *ReadgroupsetsCoveragebucketsListCall) ReferenceName(referenceName string) *ReadgroupsetsCoveragebucketsListCall

ReferenceName sets the optional parameter "referenceName": The name of the reference to query, within the reference set associated with this query.

func (*ReadgroupsetsCoveragebucketsListCall) Start 

func (c *ReadgroupsetsCoveragebucketsListCall) Start(start int64) *ReadgroupsetsCoveragebucketsListCall

Start sets the optional parameter "start": The start position of the range on the reference, 0-based inclusive. If specified, `referenceName` must also be specified. Defaults to 0.

func (*ReadgroupsetsCoveragebucketsListCall) TargetBucketWidth 

func (c *ReadgroupsetsCoveragebucketsListCall) TargetBucketWidth(targetBucketWidth int64) *ReadgroupsetsCoveragebucketsListCall

TargetBucketWidth sets the optional parameter "targetBucketWidth": 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.

type ReadgroupsetsCoveragebucketsService 

type ReadgroupsetsCoveragebucketsService struct {
	// contains filtered or unexported fields
}

func NewReadgroupsetsCoveragebucketsService 

func NewReadgroupsetsCoveragebucketsService(s *Service) *ReadgroupsetsCoveragebucketsService

func (*ReadgroupsetsCoveragebucketsService) List 

func (r *ReadgroupsetsCoveragebucketsService) List(readGroupSetId string) *ReadgroupsetsCoveragebucketsListCall

List: 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. 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.

type ReadgroupsetsDeleteCall 

type ReadgroupsetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsDeleteCall) Do 

func (c *ReadgroupsetsDeleteCall) Do() (*Empty, error)

func (*ReadgroupsetsDeleteCall) Fields 

func (c *ReadgroupsetsDeleteCall) Fields(s ...googleapi.Field) *ReadgroupsetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsExportCall 

type ReadgroupsetsExportCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsExportCall) Do 

func (c *ReadgroupsetsExportCall) Do() (*Operation, error)

func (*ReadgroupsetsExportCall) Fields 

func (c *ReadgroupsetsExportCall) Fields(s ...googleapi.Field) *ReadgroupsetsExportCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsGetCall 

type ReadgroupsetsGetCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsGetCall) Do 

func (c *ReadgroupsetsGetCall) Do() (*ReadGroupSet, error)

func (*ReadgroupsetsGetCall) Fields 

func (c *ReadgroupsetsGetCall) Fields(s ...googleapi.Field) *ReadgroupsetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsImportCall 

type ReadgroupsetsImportCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsImportCall) Do 

func (c *ReadgroupsetsImportCall) Do() (*Operation, error)

func (*ReadgroupsetsImportCall) Fields 

func (c *ReadgroupsetsImportCall) Fields(s ...googleapi.Field) *ReadgroupsetsImportCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsPatchCall 

type ReadgroupsetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsPatchCall) Do 

func (c *ReadgroupsetsPatchCall) Do() (*ReadGroupSet, error)

func (*ReadgroupsetsPatchCall) Fields 

func (c *ReadgroupsetsPatchCall) Fields(s ...googleapi.Field) *ReadgroupsetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*ReadgroupsetsPatchCall) UpdateMask 

func (c *ReadgroupsetsPatchCall) UpdateMask(updateMask string) *ReadgroupsetsPatchCall

UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. At this time, mutable fields are [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id] and [name][google.genomics.v1.ReadGroupSet.name]. Acceptable values are "referenceSetId" and "name". If unspecified, all mutable fields will be updated.

type ReadgroupsetsSearchCall 

type ReadgroupsetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReadgroupsetsSearchCall) Do 

func (c *ReadgroupsetsSearchCall) Do() (*SearchReadGroupSetsResponse, error)

func (*ReadgroupsetsSearchCall) Fields 

func (c *ReadgroupsetsSearchCall) Fields(s ...googleapi.Field) *ReadgroupsetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadgroupsetsService 

type ReadgroupsetsService struct {
	Coveragebuckets *ReadgroupsetsCoveragebucketsService
	// contains filtered or unexported fields
}

func NewReadgroupsetsService 

func NewReadgroupsetsService(s *Service) *ReadgroupsetsService

func (*ReadgroupsetsService) Delete 

func (r *ReadgroupsetsService) Delete(readGroupSetId string) *ReadgroupsetsDeleteCall

Delete: Deletes a read group set.

func (*ReadgroupsetsService) Export 

func (r *ReadgroupsetsService) Export(readGroupSetId string, exportreadgroupsetrequest *ExportReadGroupSetRequest) *ReadgroupsetsExportCall

Export: Exports a read group set to a BAM file in Google Cloud Storage. Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, some custom tags will be converted to strings, and original reference sequence order is not necessarily preserved.

func (*ReadgroupsetsService) Get 

func (r *ReadgroupsetsService) Get(readGroupSetId string) *ReadgroupsetsGetCall

Get: Gets a read group set by ID.

func (*ReadgroupsetsService) Import 

func (r *ReadgroupsetsService) Import(importreadgroupsetsrequest *ImportReadGroupSetsRequest) *ReadgroupsetsImportCall

Import: Creates read group sets by asynchronously importing the provided information. Note that currently comments in the input file header are **not** imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.

func (*ReadgroupsetsService) Patch 

func (r *ReadgroupsetsService) Patch(readGroupSetId string, readgroupset *ReadGroupSet) *ReadgroupsetsPatchCall

Patch: Updates a read group set. This method supports patch semantics.

func (*ReadgroupsetsService) Search 

func (r *ReadgroupsetsService) Search(searchreadgroupsetsrequest *SearchReadGroupSetsRequest) *ReadgroupsetsSearchCall

Search: Searches for read group sets matching the criteria. Implements [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schem as/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).

type ReadsSearchCall 

type ReadsSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReadsSearchCall) Do 

func (c *ReadsSearchCall) Do() (*SearchReadsResponse, error)

func (*ReadsSearchCall) Fields 

func (c *ReadsSearchCall) Fields(s ...googleapi.Field) *ReadsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReadsService 

type ReadsService struct {
	// contains filtered or unexported fields
}

func NewReadsService 

func NewReadsService(s *Service) *ReadsService

func (*ReadsService) Search 

func (r *ReadsService) Search(searchreadsrequest *SearchReadsRequest) *ReadsSearchCall

Search: Gets a list of reads for one or more read group sets. 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 (reference sequence & position). Reads with equivalent genomic coordinates are returned in a deterministic order. Implements [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/ v0.5.1/src/main/resources/avro/readmethods.avdl#L85).

type Reference 

type Reference struct {
	// Id: The server-generated reference ID, unique across all references.
	Id string `json:"id,omitempty"`

	// Length: The length of this reference's sequence.
	Length int64 `json:"length,omitempty,string"`

	// Md5checksum: 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 `json:"md5checksum,omitempty"`

	// Name: The name of this reference, for example `22`.
	Name string `json:"name,omitempty"`

	// NcbiTaxonId: ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g.
	// 9606->human) if not specified by the containing reference set.
	NcbiTaxonId int64 `json:"ncbiTaxonId,omitempty"`

	// SourceAccessions: All known corresponding accession IDs in INSDC
	// (GenBank/ENA/DDBJ) ideally with a version number, for example
	// `GCF_000001405.26`.
	SourceAccessions []string `json:"sourceAccessions,omitempty"`

	// SourceUri: The URI from which the sequence was obtained. Specifies a
	// FASTA format file/string with one name, sequence pair.
	SourceUri string `json:"sourceUri,omitempty"`
}

Reference: A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets.

type ReferenceBound 

type ReferenceBound struct {
	// ReferenceName: The reference the bound is associate with.
	ReferenceName string `json:"referenceName,omitempty"`

	// UpperBound: An upper bound (inclusive) on the starting coordinate of
	// any variant in the reference sequence.
	UpperBound int64 `json:"upperBound,omitempty,string"`
}

ReferenceBound: ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.

type ReferenceSet 

type ReferenceSet struct {
	// AssemblyId: Public id of this reference set, such as `GRCh37`.
	AssemblyId string `json:"assemblyId,omitempty"`

	// Description: Free text description of this reference set.
	Description string `json:"description,omitempty"`

	// Id: The server-generated reference set ID, unique across all
	// reference sets.
	Id string `json:"id,omitempty"`

	// Md5checksum: 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 `json:"md5checksum,omitempty"`

	// NcbiTaxonId: ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g.
	// 9606->human) indicating the species which this assembly 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, e.g. EBV in a human reference
	// genome.
	NcbiTaxonId int64 `json:"ncbiTaxonId,omitempty"`

	// ReferenceIds: The IDs of the reference objects that are part of this
	// set. `Reference.md5checksum` must be unique within this set.
	ReferenceIds []string `json:"referenceIds,omitempty"`

	// SourceAccessions: All known corresponding accession IDs in INSDC
	// (GenBank/ENA/DDBJ) ideally with a version number, for example
	// `NC_000001.11`.
	SourceAccessions []string `json:"sourceAccessions,omitempty"`

	// SourceUri: The URI from which the references were obtained.
	SourceUri string `json:"sourceUri,omitempty"`
}

ReferenceSet: A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.

type ReferencesBasesListCall 

type ReferencesBasesListCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesBasesListCall) Do 

func (c *ReferencesBasesListCall) Do() (*ListBasesResponse, error)

func (*ReferencesBasesListCall) End 

func (c *ReferencesBasesListCall) End(end int64) *ReferencesBasesListCall

End sets the optional parameter "end": The end position (0-based, exclusive) of this query. Defaults to the length of this reference.

func (*ReferencesBasesListCall) Fields 

func (c *ReferencesBasesListCall) Fields(s ...googleapi.Field) *ReferencesBasesListCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*ReferencesBasesListCall) PageSize 

func (c *ReferencesBasesListCall) PageSize(pageSize int64) *ReferencesBasesListCall

PageSize sets the optional parameter "pageSize": Specifies the maximum number of bases to return in a single page.

func (*ReferencesBasesListCall) PageToken 

func (c *ReferencesBasesListCall) PageToken(pageToken string) *ReferencesBasesListCall

PageToken sets the optional parameter "pageToken": 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.

func (*ReferencesBasesListCall) Start 

func (c *ReferencesBasesListCall) Start(start int64) *ReferencesBasesListCall

Start sets the optional parameter "start": The start position (0-based) of this query. Defaults to 0.

type ReferencesBasesService 

type ReferencesBasesService struct {
	// contains filtered or unexported fields
}

func NewReferencesBasesService 

func NewReferencesBasesService(s *Service) *ReferencesBasesService

func (*ReferencesBasesService) List 

func (r *ReferencesBasesService) List(referenceId string) *ReferencesBasesListCall

List: Lists the bases in a reference, optionally restricted to a range. Implements [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas /blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).

type ReferencesGetCall 

type ReferencesGetCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesGetCall) Do 

func (c *ReferencesGetCall) Do() (*Reference, error)

func (*ReferencesGetCall) Fields 

func (c *ReferencesGetCall) Fields(s ...googleapi.Field) *ReferencesGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesSearchCall 

type ReferencesSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesSearchCall) Do 

func (c *ReferencesSearchCall) Do() (*SearchReferencesResponse, error)

func (*ReferencesSearchCall) Fields 

func (c *ReferencesSearchCall) Fields(s ...googleapi.Field) *ReferencesSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesService 

type ReferencesService struct {
	Bases *ReferencesBasesService
	// contains filtered or unexported fields
}

func NewReferencesService 

func NewReferencesService(s *Service) *ReferencesService

func (*ReferencesService) Get 

func (r *ReferencesService) Get(referenceId string) *ReferencesGetCall

Get: Gets a reference. Implements [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob /v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).

func (*ReferencesService) Search 

func (r *ReferencesService) Search(searchreferencesrequest *SearchReferencesRequest) *ReferencesSearchCall

Search: Searches for references which match the given criteria. Implements [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/ blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).

type ReferencesetsGetCall 

type ReferencesetsGetCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesetsGetCall) Do 

func (c *ReferencesetsGetCall) Do() (*ReferenceSet, error)

func (*ReferencesetsGetCall) Fields 

func (c *ReferencesetsGetCall) Fields(s ...googleapi.Field) *ReferencesetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesetsSearchCall 

type ReferencesetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*ReferencesetsSearchCall) Do 

func (c *ReferencesetsSearchCall) Do() (*SearchReferenceSetsResponse, error)

func (*ReferencesetsSearchCall) Fields 

func (c *ReferencesetsSearchCall) Fields(s ...googleapi.Field) *ReferencesetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type ReferencesetsService 

type ReferencesetsService struct {
	// contains filtered or unexported fields
}

func NewReferencesetsService 

func NewReferencesetsService(s *Service) *ReferencesetsService

func (*ReferencesetsService) Get 

func (r *ReferencesetsService) Get(referenceSetId string) *ReferencesetsGetCall

Get: Gets a reference set. Implements [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/b lob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).

func (*ReferencesetsService) Search 

func (r *ReferencesetsService) Search(searchreferencesetsrequest *SearchReferenceSetsRequest) *ReferencesetsSearchCall

Search: Searches for reference sets which match the given criteria. Implements [GlobalAllianceApi.searchReferenceSets](http://ga4gh.org/documentation /api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSets).

type SearchCallSetsRequest 

type SearchCallSetsRequest struct {
	// Name: Only return call sets for which a substring of the name matches
	// this string.
	Name string `json:"name,omitempty"`

	// PageSize: The maximum number of call sets to return. If unspecified,
	// defaults to 1000.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: 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 `json:"pageToken,omitempty"`

	// VariantSetIds: Restrict the query to call sets within the given
	// variant sets. At least one ID must be provided.
	VariantSetIds []string `json:"variantSetIds,omitempty"`
}

SearchCallSetsRequest: The call set search request.

type SearchCallSetsResponse 

type SearchCallSetsResponse struct {
	// CallSets: The list of matching call sets.
	CallSets []*CallSet `json:"callSets,omitempty"`

	// NextPageToken: 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 `json:"nextPageToken,omitempty"`
}

SearchCallSetsResponse: The call set search response.

type SearchReadGroupSetsRequest 

type SearchReadGroupSetsRequest struct {
	// DatasetIds: Restricts this query to read group sets within the given
	// datasets. At least one ID must be provided.
	DatasetIds []string `json:"datasetIds,omitempty"`

	// Name: Only return read group sets for which a substring of the name
	// matches this string.
	Name string `json:"name,omitempty"`

	// PageSize: Specifies number of results to return in a single page. If
	// unspecified, it will default to 256. The maximum value is 1024.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: 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 `json:"pageToken,omitempty"`
}

SearchReadGroupSetsRequest: The read group set search request.

type SearchReadGroupSetsResponse 

type SearchReadGroupSetsResponse struct {
	// NextPageToken: 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 `json:"nextPageToken,omitempty"`

	// ReadGroupSets: The list of matching read group sets.
	ReadGroupSets []*ReadGroupSet `json:"readGroupSets,omitempty"`
}

SearchReadGroupSetsResponse: The read group set search response.

type SearchReadsRequest 

type SearchReadsRequest struct {
	// End: The end position of the range on the reference, 0-based
	// exclusive. If specified, `referenceName` must also be specified.
	End int64 `json:"end,omitempty,string"`

	// PageSize: Specifies number of results to return in a single page. If
	// unspecified, it will default to 256. The maximum value is 2048.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: 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 `json:"pageToken,omitempty"`

	// ReadGroupIds: 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 `json:"readGroupIds,omitempty"`

	// ReadGroupSetIds: 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 `json:"readGroupSetIds,omitempty"`

	// ReferenceName: The reference sequence name, for example `chr1`, `1`,
	// or `chrX`. If set to *, only unmapped reads are returned.
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The start position of the range on the reference, 0-based
	// inclusive. If specified, `referenceName` must also be specified.
	Start int64 `json:"start,omitempty,string"`
}

SearchReadsRequest: The read search request.

type SearchReadsResponse 

type SearchReadsResponse struct {
	// Alignments: 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 last and are
	// further sorted in ascending lexicographic order by fragment name.
	Alignments []*Read `json:"alignments,omitempty"`

	// NextPageToken: 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 `json:"nextPageToken,omitempty"`
}

SearchReadsResponse: The read search response.

type SearchReferenceSetsRequest 

type SearchReferenceSetsRequest struct {
	// Accessions: If present, return references for which the accession
	// matches any of these strings. Best to give a version number, for
	// example `GCF_000001405.26`. If only the main accession number is
	// given then all records with that main accession will be returned,
	// whichever version. Note that different versions will have different
	// sequences.
	Accessions []string `json:"accessions,omitempty"`

	// AssemblyId: If present, return reference sets for which a substring
	// of their `assemblyId` matches this string (case insensitive).
	AssemblyId string `json:"assemblyId,omitempty"`

	// Md5checksums: If present, return references for which the
	// `md5checksum` matches. See `ReferenceSet.md5checksum` for details.
	Md5checksums []string `json:"md5checksums,omitempty"`

	// PageSize: Specifies the maximum number of results to return in a
	// single page.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: 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 `json:"pageToken,omitempty"`
}

type SearchReferenceSetsResponse 

type SearchReferenceSetsResponse struct {
	// NextPageToken: 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 `json:"nextPageToken,omitempty"`

	// ReferenceSets: The matching references sets.
	ReferenceSets []*ReferenceSet `json:"referenceSets,omitempty"`
}

type SearchReferencesRequest 

type SearchReferencesRequest struct {
	// Accessions: If present, return references for which the accession
	// matches this string. Best to give a version number, for example
	// `GCF_000001405.26`. If only the main accession number is given then
	// all records with that main accession will be returned, whichever
	// version. Note that different versions will have different sequences.
	Accessions []string `json:"accessions,omitempty"`

	// Md5checksums: If present, return references for which the
	// `md5checksum` matches. See `Reference.md5checksum` for construction
	// details.
	Md5checksums []string `json:"md5checksums,omitempty"`

	// PageSize: Specifies the maximum number of results to return in a
	// single page.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: 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 `json:"pageToken,omitempty"`

	// ReferenceSetId: If present, return only references which belong to
	// this reference set.
	ReferenceSetId string `json:"referenceSetId,omitempty"`
}

type SearchReferencesResponse 

type SearchReferencesResponse struct {
	// NextPageToken: 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 `json:"nextPageToken,omitempty"`

	// References: The matching references.
	References []*Reference `json:"references,omitempty"`
}

type SearchVariantSetsRequest 

type SearchVariantSetsRequest struct {
	// DatasetIds: Exactly one dataset ID must be provided here. Only
	// variant sets which belong to this dataset will be returned.
	DatasetIds []string `json:"datasetIds,omitempty"`

	// PageSize: The maximum number of variant sets to return in a request.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: 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 `json:"pageToken,omitempty"`
}

SearchVariantSetsRequest: The search variant sets request.

type SearchVariantSetsResponse 

type SearchVariantSetsResponse struct {
	// NextPageToken: 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 `json:"nextPageToken,omitempty"`

	// VariantSets: The variant sets belonging to the requested dataset.
	VariantSets []*VariantSet `json:"variantSets,omitempty"`
}

SearchVariantSetsResponse: The search variant sets response.

type SearchVariantsRequest 

type SearchVariantsRequest struct {
	// CallSetIds: 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. Currently, variants with no calls from any call set
	// will never be returned.
	CallSetIds []string `json:"callSetIds,omitempty"`

	// End: The end of the window, 0-based exclusive. If unspecified or 0,
	// defaults to the length of the reference.
	End int64 `json:"end,omitempty,string"`

	// MaxCalls: The maximum number of calls to return. However, at least
	// one variant will always be returned, even if it has more calls than
	// this limit. If unspecified, defaults to 5000.
	MaxCalls int64 `json:"maxCalls,omitempty"`

	// PageSize: The maximum number of variants to return. If unspecified,
	// defaults to 5000.
	PageSize int64 `json:"pageSize,omitempty"`

	// PageToken: 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 `json:"pageToken,omitempty"`

	// ReferenceName: Required. Only return variants in this reference
	// sequence.
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The beginning of the window (0-based, inclusive) for which
	// overlapping variants should be returned. If unspecified, defaults to
	// 0.
	Start int64 `json:"start,omitempty,string"`

	// VariantName: Only return variants which have exactly this name.
	VariantName string `json:"variantName,omitempty"`

	// VariantSetIds: 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 `json:"variantSetIds,omitempty"`
}

SearchVariantsRequest: The variant search request.

type SearchVariantsResponse 

type SearchVariantsResponse struct {
	// NextPageToken: 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 `json:"nextPageToken,omitempty"`

	// Variants: The list of matching Variants.
	Variants []*Variant `json:"variants,omitempty"`
}

SearchVariantsResponse: The variant search response.

type Service 

type Service struct {
	BasePath  string // API endpoint base URL
	UserAgent string // optional additional User-Agent fragment

	Callsets *CallsetsService

	Datasets *DatasetsService

	Operations *OperationsService

	Readgroupsets *ReadgroupsetsService

	Reads *ReadsService

	References *ReferencesService

	Referencesets *ReferencesetsService

	Variants *VariantsService

	Variantsets *VariantsetsService
	// contains filtered or unexported fields
}

func New 

func New(client *http.Client) (*Service, error)

type Status 

type Status struct {
	// Code: The status code, which should be an enum value of
	// [google.rpc.Code][google.rpc.Code].
	Code int64 `json:"code,omitempty"`

	// Details: A list of messages that carry the error details. There will
	// be a common set of message types for APIs to use.
	Details []StatusDetails `json:"details,omitempty"`

	// Message: 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][google.rpc.Status.details] field,
	// or localized by the client.
	Message string `json:"message,omitempty"`
}

Status: The `Status` defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by [gRPC](https://github.com/grpc). The error model is designed to be: - Simple to use and understand for most users. - Flexible enough to meet unexpected needs. # Overview The `Status` message contains 3 pieces of data: error code, error message, and error details. The error code should be an enum value of [google.rpc.Code][google.rpc.Code], but it may accept additional error codes if needed. The error message should be a developer-facing English message that helps developers *understand* and *resolve* the error. If a localized user-facing error message is needed, it can be sent in the error details or localized by the client. The optional error details may contain arbitrary information about the error. There is a predefined set of error detail types in the package `google.rpc` which can be used for common error conditions. # Language mapping The `Status` message is the logical representation of the error model, but it is not necessarily the actual wire format. When the `Status` message is exposed in different client libraries and different wire protocols, it can be mapped differently. For example, it will likely be mapped to some exceptions in Java, but more likely mapped to some error codes in C. # Other uses The error model and the `Status` message can be used in a variety of environments - either with or without APIs - to provide consistent developer experience across different environments. Example uses of this error model include: - Partial errors. If a service needs to return partial errors to the client, it may embed the `Status` in the normal response to indicate the partial errors. - Workflow errors. A typical workflow has multiple steps. Each step may have a `Status` message for error reporting purpose. - Batch operations. If a client uses batch request and batch response, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds asynchronous operation results in its response, the status of those operations should be represented directly using the `Status` message. - Logging. If some API errors are stored in logs, the message `Status` could be used directly after any stripping needed for security/privacy reasons.

type StatusDetails 

type StatusDetails interface{}

type UndeleteDatasetRequest 

type UndeleteDatasetRequest struct {
}

type Variant 

type Variant struct {
	// AlternateBases: The bases that appear instead of the reference bases.
	AlternateBases []string `json:"alternateBases,omitempty"`

	// Calls: The variant calls for this particular variant. Each one
	// represents the determination of genotype with respect to this
	// variant.
	Calls []*VariantCall `json:"calls,omitempty"`

	// Created: The date this variant was created, in milliseconds from the
	// epoch.
	Created int64 `json:"created,omitempty,string"`

	// End: 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 int64 `json:"end,omitempty,string"`

	// Filter: A list of filters (normally quality filters) this variant has
	// failed. `PASS` indicates this variant has passed all filters.
	Filter []string `json:"filter,omitempty"`

	// Id: The server-generated variant ID, unique across all variants.
	Id string `json:"id,omitempty"`

	// Info: A map of additional variant information. This must be of the
	// form map (string key mapping to a list of string values).
	Info *VariantInfo `json:"info,omitempty"`

	// Names: Names for the variant, for example a RefSNP ID.
	Names []string `json:"names,omitempty"`

	// Quality: A measure of how likely this variant is to be real. A higher
	// value is better.
	Quality float64 `json:"quality,omitempty"`

	// ReferenceBases: The reference bases for this variant. They start at
	// the given position.
	ReferenceBases string `json:"referenceBases,omitempty"`

	// ReferenceName: The reference on which this variant occurs. (such as
	// `chr20` or `X`)
	ReferenceName string `json:"referenceName,omitempty"`

	// Start: The position at which this variant occurs (0-based). This
	// corresponds to the first base of the string of reference bases.
	Start int64 `json:"start,omitempty,string"`

	// VariantSetId: The ID of the variant set this variant belongs to.
	VariantSetId string `json:"variantSetId,omitempty"`
}

Variant: A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.

type VariantCall 

type VariantCall struct {
	// CallSetId: The ID of the call set this variant call belongs to.
	CallSetId string `json:"callSetId,omitempty"`

	// CallSetName: The name of the call set this variant call belongs to.
	CallSetName string `json:"callSetName,omitempty"`

	// Genotype: 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 []int64 `json:"genotype,omitempty"`

	// GenotypeLikelihood: 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 []float64 `json:"genotypeLikelihood,omitempty"`

	// Info: A map of additional variant call information. This must be of
	// the form map (string key mapping to a list of string values).
	Info *VariantCallInfo `json:"info,omitempty"`

	// Phaseset: 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 `json:"phaseset,omitempty"`
}

VariantCall: A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.

type VariantCallInfo 

type VariantCallInfo struct {
}

VariantCallInfo: A map of additional variant call information. This must be of the form map (string key mapping to a list of string values).

type VariantInfo 

type VariantInfo struct {
}

VariantInfo: A map of additional variant information. This must be of the form map (string key mapping to a list of string values).

type VariantSet 

type VariantSet struct {
	// DatasetId: The dataset to which this variant set belongs.
	DatasetId string `json:"datasetId,omitempty"`

	// Id: The server-generated variant set ID, unique across all variant
	// sets.
	Id string `json:"id,omitempty"`

	// Metadata: The metadata associated with this variant set.
	Metadata []*VariantSetMetadata `json:"metadata,omitempty"`

	// ReferenceBounds: A list of all references used by the variants in a
	// variant set with associated coordinate upper bounds for each one.
	ReferenceBounds []*ReferenceBound `json:"referenceBounds,omitempty"`
}

VariantSet: A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.

type VariantSetMetadata 

type VariantSetMetadata struct {
	// Description: A textual description of this metadata.
	Description string `json:"description,omitempty"`

	// Id: 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 `json:"id,omitempty"`

	// Info: Remaining structured metadata key-value pairs. This must be of
	// the form map (string key mapping to a list of string values).
	Info *VariantSetMetadataInfo `json:"info,omitempty"`

	// Key: The top-level key.
	Key string `json:"key,omitempty"`

	// Number: The number of values that can be included in a field
	// described by this metadata.
	Number int64 `json:"number,omitempty"`

	// Type: The type of data. Possible types include: Integer, Float, Flag,
	// Character, and String.
	//
	// Possible values:
	//   "TYPE_UNSPECIFIED"
	//   "INTEGER"
	//   "FLOAT"
	//   "FLAG"
	//   "CHARACTER"
	//   "STRING"
	Type string `json:"type,omitempty"`

	// Value: The value field for simple metadata
	Value string `json:"value,omitempty"`
}

VariantSetMetadata: Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.

type VariantSetMetadataInfo 

type VariantSetMetadataInfo struct {
}

VariantSetMetadataInfo: Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).

type VariantsCreateCall 

type VariantsCreateCall struct {
	// contains filtered or unexported fields
}

func (*VariantsCreateCall) Do 

func (c *VariantsCreateCall) Do() (*Variant, error)

func (*VariantsCreateCall) Fields 

func (c *VariantsCreateCall) Fields(s ...googleapi.Field) *VariantsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsDeleteCall 

type VariantsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*VariantsDeleteCall) Do 

func (c *VariantsDeleteCall) Do() (*Empty, error)

func (*VariantsDeleteCall) Fields 

func (c *VariantsDeleteCall) Fields(s ...googleapi.Field) *VariantsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsGetCall 

type VariantsGetCall struct {
	// contains filtered or unexported fields
}

func (*VariantsGetCall) Do 

func (c *VariantsGetCall) Do() (*Variant, error)

func (*VariantsGetCall) Fields 

func (c *VariantsGetCall) Fields(s ...googleapi.Field) *VariantsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsImportCall 

type VariantsImportCall struct {
	// contains filtered or unexported fields
}

func (*VariantsImportCall) Do 

func (c *VariantsImportCall) Do() (*Operation, error)

func (*VariantsImportCall) Fields 

func (c *VariantsImportCall) Fields(s ...googleapi.Field) *VariantsImportCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsMergeCall 

type VariantsMergeCall struct {
	// contains filtered or unexported fields
}

func (*VariantsMergeCall) Do 

func (c *VariantsMergeCall) Do() (*Empty, error)

func (*VariantsMergeCall) Fields 

func (c *VariantsMergeCall) Fields(s ...googleapi.Field) *VariantsMergeCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsPatchCall 

type VariantsPatchCall struct {
	// contains filtered or unexported fields
}

func (*VariantsPatchCall) Do 

func (c *VariantsPatchCall) Do() (*Variant, error)

func (*VariantsPatchCall) Fields 

func (c *VariantsPatchCall) Fields(s ...googleapi.Field) *VariantsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*VariantsPatchCall) UpdateMask 

func (c *VariantsPatchCall) UpdateMask(updateMask string) *VariantsPatchCall

UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. At this time, mutable fields are [names][google.genomics.v1.Variant.names] and [info][google.genomics.v1.Variant.info]. Acceptable values are "names" and "info". If unspecified, all mutable fields will be updated.

type VariantsSearchCall 

type VariantsSearchCall struct {
	// contains filtered or unexported fields
}

func (*VariantsSearchCall) Do 

func (c *VariantsSearchCall) Do() (*SearchVariantsResponse, error)

func (*VariantsSearchCall) Fields 

func (c *VariantsSearchCall) Fields(s ...googleapi.Field) *VariantsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsService 

type VariantsService struct {
	// contains filtered or unexported fields
}

func NewVariantsService 

func NewVariantsService(s *Service) *VariantsService

func (*VariantsService) Create 

func (r *VariantsService) Create(variant *Variant) *VariantsCreateCall

Create: Creates a new variant.

func (*VariantsService) Delete 

func (r *VariantsService) Delete(variantId string) *VariantsDeleteCall

Delete: Deletes a variant.

func (*VariantsService) Get 

func (r *VariantsService) Get(variantId string) *VariantsGetCall

Get: Gets a variant by ID.

func (*VariantsService) Import 

func (r *VariantsService) Import(importvariantsrequest *ImportVariantsRequest) *VariantsImportCall

Import: Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. 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.

func (*VariantsService) Merge 

func (r *VariantsService) Merge(mergevariantsrequest *MergeVariantsRequest) *VariantsMergeCall

Merge: Merges the given variants with existing variants. 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, and other fields (such as key/value pairs) are discarded.

func (*VariantsService) Patch 

func (r *VariantsService) Patch(variantId string, variant *Variant) *VariantsPatchCall

Patch: Updates a variant. This method supports patch semantics. Returns the modified variant without its calls.

func (*VariantsService) Search 

func (r *VariantsService) Search(searchvariantsrequest *SearchVariantsRequest) *VariantsSearchCall

Search: Gets a list of variants matching the criteria. Implements [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/bl ob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).

type VariantsetsCreateCall 

type VariantsetsCreateCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsCreateCall) Do 

func (c *VariantsetsCreateCall) Do() (*VariantSet, error)

func (*VariantsetsCreateCall) Fields 

func (c *VariantsetsCreateCall) Fields(s ...googleapi.Field) *VariantsetsCreateCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsDeleteCall 

type VariantsetsDeleteCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsDeleteCall) Do 

func (c *VariantsetsDeleteCall) Do() (*Empty, error)

func (*VariantsetsDeleteCall) Fields 

func (c *VariantsetsDeleteCall) Fields(s ...googleapi.Field) *VariantsetsDeleteCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsExportCall 

type VariantsetsExportCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsExportCall) Do 

func (c *VariantsetsExportCall) Do() (*Operation, error)

func (*VariantsetsExportCall) Fields 

func (c *VariantsetsExportCall) Fields(s ...googleapi.Field) *VariantsetsExportCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsGetCall 

type VariantsetsGetCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsGetCall) Do 

func (c *VariantsetsGetCall) Do() (*VariantSet, error)

func (*VariantsetsGetCall) Fields 

func (c *VariantsetsGetCall) Fields(s ...googleapi.Field) *VariantsetsGetCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsPatchCall 

type VariantsetsPatchCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsPatchCall) Do 

func (c *VariantsetsPatchCall) Do() (*VariantSet, error)

func (*VariantsetsPatchCall) Fields 

func (c *VariantsetsPatchCall) Fields(s ...googleapi.Field) *VariantsetsPatchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

func (*VariantsetsPatchCall) UpdateMask 

func (c *VariantsetsPatchCall) UpdateMask(updateMask string) *VariantsetsPatchCall

UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. At this time, the only mutable field is [metadata][google.genomics.v1.VariantSet.metadata]. The only acceptable value is "metadata". If unspecified, all mutable fields will be updated.

type VariantsetsSearchCall 

type VariantsetsSearchCall struct {
	// contains filtered or unexported fields
}

func (*VariantsetsSearchCall) Do 

func (c *VariantsetsSearchCall) Do() (*SearchVariantSetsResponse, error)

func (*VariantsetsSearchCall) Fields 

func (c *VariantsetsSearchCall) Fields(s ...googleapi.Field) *VariantsetsSearchCall

Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.

type VariantsetsService 

type VariantsetsService struct {
	// contains filtered or unexported fields
}

func NewVariantsetsService 

func NewVariantsetsService(s *Service) *VariantsetsService

func (*VariantsetsService) Create 

func (r *VariantsetsService) Create(variantset *VariantSet) *VariantsetsCreateCall

Create: Creates a new variant set.

func (*VariantsetsService) Delete 

func (r *VariantsetsService) Delete(variantSetId string) *VariantsetsDeleteCall

Delete: Deletes the contents of a variant set. The variant set object is not deleted.

func (*VariantsetsService) Export 

func (r *VariantsetsService) Export(variantSetId string, exportvariantsetrequest *ExportVariantSetRequest) *VariantsetsExportCall

Export: Exports variant set data to an external destination.

func (*VariantsetsService) Get 

func (r *VariantsetsService) Get(variantSetId string) *VariantsetsGetCall

Get: Gets a variant set by ID.

func (*VariantsetsService) Patch 

func (r *VariantsetsService) Patch(variantSetId string, variantset *VariantSet) *VariantsetsPatchCall

Patch: Updates a variant set. This method supports patch semantics.

func (*VariantsetsService) Search 

func (r *VariantsetsService) Search(searchvariantsetsrequest *SearchVariantSetsRequest) *VariantsetsSearchCall

Search: Returns a list of all variant sets matching search criteria. Implements [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas /blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).

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