genomics

package
v0.0.0-...-ee91799 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Aug 20, 2015 License: BSD-3-Clause Imports: 11 Imported by: 0

Documentation

Overview

Package genomics provides access to the Genomics API.

See https://developers.google.com/genomics/v1beta/reference

Usage example: 

import "google.golang.org/api/genomics/v1beta"
...
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"

	// Manage your data in Google Cloud Storage
	DevstorageRead_writeScope = "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 Call 

type Call 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.
	Info map[string][]string `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"`
}

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 Google generated ID of the call set, immutable.
	Id string `json:"id,omitempty"`

	// Info: A map of additional call set information.
	Info map[string][]string `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"`
}

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() 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.

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.

func (*CallsetsService) Update 

func (r *CallsetsService) Update(callSetId string, callset *CallSet) *CallsetsUpdateCall

Update: Updates a call set.

type CallsetsUpdateCall 

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

func (*CallsetsUpdateCall) Do 

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

func (*CallsetsUpdateCall) Fields 

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

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

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 *GenomicRange `json:"range,omitempty"`
}

type Dataset 

type Dataset struct {
	// Id: The Google generated ID of the dataset, immutable.
	Id string `json:"id,omitempty"`

	// IsPublic: Flag indicating whether or not a dataset is publicly
	// viewable. If a dataset is not public, it inherits viewing permissions
	// from its project.
	IsPublic bool `json:"isPublic,omitempty"`

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

	// ProjectId: The Google Developers Console project number that this
	// dataset belongs to.
	ProjectId int64 `json:"projectId,omitempty,string"`
}

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() 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) MaxResults 

func (c *DatasetsListCall) MaxResults(maxResults uint64) *DatasetsListCall

MaxResults sets the optional parameter "maxResults": The maximum number of results returned by this request.

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 int64) *DatasetsListCall

ProjectId sets the optional parameter "projectId": Only return datasets which belong to this Google Developers Console project. Only accepts project numbers. Returns all public projects if no project number is specified.

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.

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 all datasets.

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) *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.

func (*DatasetsService) Update 

func (r *DatasetsService) Update(datasetId string, dataset *Dataset) *DatasetsUpdateCall

Update: Updates a dataset.

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 DatasetsUpdateCall 

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

func (*DatasetsUpdateCall) Do 

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

func (*DatasetsUpdateCall) Fields 

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

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

type ExperimentalCreateJobRequest 

type ExperimentalCreateJobRequest struct {
	// Align: Specifies whether or not to run the alignment pipeline. Either
	// align or callVariants must be set.
	Align bool `json:"align,omitempty"`

	// CallVariants: Specifies whether or not to run the variant calling
	// pipeline. Either align or callVariants must be set.
	CallVariants bool `json:"callVariants,omitempty"`

	// GcsOutputPath: Specifies where to copy the results of certain
	// pipelines. This should be in the form of gs://bucket/path.
	GcsOutputPath string `json:"gcsOutputPath,omitempty"`

	// PairedSourceUris: A list of Google Cloud Storage URIs of paired end
	// .fastq files to operate upon. If specified, this represents the
	// second file of each paired .fastq file. The first file of each pair
	// should be specified in sourceUris.
	PairedSourceUris []string `json:"pairedSourceUris,omitempty"`

	// ProjectId: Required. The Google Cloud Project ID with which to
	// associate the request.
	ProjectId int64 `json:"projectId,omitempty,string"`

	// SourceUris: A list of Google Cloud Storage URIs of data files to
	// operate upon. These can be .bam, interleaved .fastq, or paired
	// .fastq. If specifying paired .fastq files, the first of each pair of
	// files should be listed here, and the second of each pair should be
	// listed in pairedSourceUris.
	SourceUris []string `json:"sourceUris,omitempty"`
}

type ExperimentalCreateJobResponse 

type ExperimentalCreateJobResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type ExperimentalJobsCreateCall 

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

func (*ExperimentalJobsCreateCall) Do 

func (c *ExperimentalJobsCreateCall) Do() (*ExperimentalCreateJobResponse, error)

func (*ExperimentalJobsCreateCall) Fields 

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

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

type ExperimentalJobsService 

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

func NewExperimentalJobsService 

func NewExperimentalJobsService(s *Service) *ExperimentalJobsService

func (*ExperimentalJobsService) Create 

func (r *ExperimentalJobsService) Create(experimentalcreatejobrequest *ExperimentalCreateJobRequest) *ExperimentalJobsCreateCall

Create: Creates and asynchronously runs an ad-hoc job. This is an experimental call and may be removed or changed at any time.

type ExperimentalService 

type ExperimentalService struct {
	Jobs *ExperimentalJobsService
	// contains filtered or unexported fields
}

func NewExperimentalService 

func NewExperimentalService(s *Service) *ExperimentalService

type ExportReadsetsRequest 

type ExportReadsetsRequest struct {
	// ExportUri: A Google Cloud Storage URI where the exported BAM file
	// will be created. The currently authenticated user must have write
	// access to the new file location. An error will be returned if the URI
	// already contains data.
	ExportUri string `json:"exportUri,omitempty"`

	// ProjectId: The Google Developers Console project number that owns
	// this export.
	ProjectId int64 `json:"projectId,omitempty,string"`

	// ReadsetIds: The IDs of the readsets to export.
	ReadsetIds []string `json:"readsetIds,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"`
}

type ExportReadsetsResponse 

type ExportReadsetsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type ExportVariantsRequest 

type ExportVariantsRequest struct {
	// BigqueryDataset: The BigQuery dataset to export data to. Note that
	// this is distinct from the Genomics concept of "dataset".
	BigqueryDataset string `json:"bigqueryDataset,omitempty"`

	// BigqueryTable: 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.
	Format string `json:"format,omitempty"`

	// ProjectId: The Google Cloud project number 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 int64 `json:"projectId,omitempty,string"`

	// VariantSetId: Required. The ID of the variant set that contains
	// variant data which should be exported. The caller must have READ
	// access to this variant set.
	VariantSetId string `json:"variantSetId,omitempty"`
}

type ExportVariantsResponse 

type ExportVariantsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type GenomicRange 

type GenomicRange struct {
	// SequenceEnd: The end position of the range on the reference, 1-based
	// exclusive. If specified, sequenceName must also be specified.
	SequenceEnd uint64 `json:"sequenceEnd,omitempty,string"`

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

	// SequenceStart: The start position of the range on the reference,
	// 1-based inclusive. If specified, sequenceName must also be specified.
	SequenceStart uint64 `json:"sequenceStart,omitempty,string"`
}
type Header struct {
	// SortingOrder: (SO) Sorting order of alignments.
	SortingOrder string `json:"sortingOrder,omitempty"`

	// Version: (VN) BAM format version.
	Version string `json:"version,omitempty"`
}

type HeaderSection 

type HeaderSection struct {
	// Comments: (@CO) One-line text comments.
	Comments []string `json:"comments,omitempty"`

	// FileUri: [Deprecated] This field is deprecated and will no longer be
	// populated. Please use filename instead.
	FileUri string `json:"fileUri,omitempty"`

	// Filename: The name of the file from which this data was imported.
	Filename string `json:"filename,omitempty"`

	// Headers: (@HD) The header line.
	Headers []*Header `json:"headers,omitempty"`

	// Programs: (@PG) Programs.
	Programs []*Program `json:"programs,omitempty"`

	// ReadGroups: (@RG) Read group.
	ReadGroups []*ReadGroup `json:"readGroups,omitempty"`

	// RefSequences: (@SQ) Reference sequence dictionary.
	RefSequences []*ReferenceSequence `json:"refSequences,omitempty"`
}

type ImportReadsetsRequest 

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

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

type ImportReadsetsResponse 

type ImportReadsetsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type ImportVariantsRequest 

type ImportVariantsRequest struct {
	// Format: The format of the variant data being imported.
	Format string `json:"format,omitempty"`

	// SourceUris: A list of URIs pointing at VCF files in Google Cloud
	// Storage. See the VCF Specification for more details on the input
	// format.
	SourceUris []string `json:"sourceUris,omitempty"`

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

type ImportVariantsResponse 

type ImportVariantsResponse struct {
	// JobId: A job ID that can be used to get status information.
	JobId string `json:"jobId,omitempty"`
}

type Job 

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

	// Description: A more detailed description of this job's current
	// status.
	Description string `json:"description,omitempty"`

	// Errors: Any errors that occurred during processing.
	Errors []string `json:"errors,omitempty"`

	// Id: The job ID.
	Id string `json:"id,omitempty"`

	// ImportedIds: If this Job represents an import, this field will
	// contain the IDs of the objects that were successfully imported.
	ImportedIds []string `json:"importedIds,omitempty"`

	// ProjectId: The Google Developers Console project number to which this
	// job belongs.
	ProjectId int64 `json:"projectId,omitempty,string"`

	// Request: A summarized representation of the original service request.
	Request *JobRequest `json:"request,omitempty"`

	// Status: The status of this job.
	Status string `json:"status,omitempty"`

	// Warnings: Any warnings that occurred during processing.
	Warnings []string `json:"warnings,omitempty"`
}

type JobRequest 

type JobRequest struct {
	// Destination: The data destination of the request, for example, a
	// Google BigQuery Table or Dataset ID.
	Destination []string `json:"destination,omitempty"`

	// Source: The data source of the request, for example, a Google Cloud
	// Storage object path or Readset ID.
	Source []string `json:"source,omitempty"`

	// Type: The original request type.
	Type string `json:"type,omitempty"`
}

type JobsCancelCall 

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

func (*JobsCancelCall) Do 

func (c *JobsCancelCall) Do() error

func (*JobsCancelCall) Fields 

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

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

type JobsGetCall 

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

func (*JobsGetCall) Do 

func (c *JobsGetCall) Do() (*Job, error)

func (*JobsGetCall) Fields 

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

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

type JobsSearchCall 

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

func (*JobsSearchCall) Do 

func (c *JobsSearchCall) Do() (*SearchJobsResponse, error)

func (*JobsSearchCall) Fields 

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

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

type JobsService 

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

func NewJobsService 

func NewJobsService(s *Service) *JobsService

func (*JobsService) Cancel 

func (r *JobsService) Cancel(jobId string) *JobsCancelCall

Cancel: Cancels a job by ID. Note that it is possible for partial results to be generated and stored for cancelled jobs.

func (*JobsService) Get 

func (r *JobsService) Get(jobId string) *JobsGetCall

Get: Gets a job by ID.

func (*JobsService) Search 

func (r *JobsService) Search(searchjobsrequest *SearchJobsRequest) *JobsSearchCall

Search: Gets a list of jobs matching the criteria.

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 uint64 `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"`
}

type MergeVariantsRequest 

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

type Metadata 

type Metadata 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.
	Info map[string][]string `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 string `json:"number,omitempty"`

	// Type: The type of data. Possible types include: Integer, Float, Flag,
	// Character, and String.
	Type string `json:"type,omitempty"`

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

type Program 

type Program struct {
	// CommandLine: (CL) Command line.
	CommandLine string `json:"commandLine,omitempty"`

	// Id: (ID) Program record identifier.
	Id string `json:"id,omitempty"`

	// Name: (PN) Program name.
	Name string `json:"name,omitempty"`

	// PrevProgramId: (PP) Previous program ID.
	PrevProgramId string `json:"prevProgramId,omitempty"`

	// Version: (VN) Program version.
	Version string `json:"version,omitempty"`
}

type Read 

type Read struct {
	// AlignedBases: The originalBases after the cigar field has been
	// applied. Deletions are represented with '-' and insertions are
	// omitted.
	AlignedBases string `json:"alignedBases,omitempty"`

	// BaseQuality: Represents the quality of each base in this read. Each
	// character represents one base. To get the quality, take the ASCII
	// value of the character and subtract 33. (QUAL)
	BaseQuality string `json:"baseQuality,omitempty"`

	// Cigar: A condensed representation of how this read matches up to the
	// reference. (CIGAR)
	Cigar string `json:"cigar,omitempty"`

	// Flags: Each bit of this number has a different meaning if enabled.
	// See the full BAM spec for more details. (FLAG)
	Flags int64 `json:"flags,omitempty"`

	// Id: The Google generated ID of the read, immutable.
	Id string `json:"id,omitempty"`

	// MappingQuality: A score up to 255 that represents how likely this
	// read's aligned position is to be correct. A higher value is better.
	// (MAPQ)
	MappingQuality int64 `json:"mappingQuality,omitempty"`

	// MatePosition: The 1-based start position of the paired read. (PNEXT)
	MatePosition int64 `json:"matePosition,omitempty"`

	// MateReferenceSequenceName: The name of the sequence that the paired
	// read is aligned to. This is usually the same as
	// referenceSequenceName. (RNEXT)
	MateReferenceSequenceName string `json:"mateReferenceSequenceName,omitempty"`

	// Name: The name of the read. When imported from a BAM file, this is
	// the query template name. (QNAME)
	Name string `json:"name,omitempty"`

	// OriginalBases: The list of bases that this read represents (such as
	// "CATCGA"). (SEQ)
	OriginalBases string `json:"originalBases,omitempty"`

	// Position: The 1-based start position of the aligned read. If the
	// first base starts at the very beginning of the reference sequence,
	// then the position would be '1'. (POS)
	Position int64 `json:"position,omitempty"`

	// ReadsetId: The ID of the readset this read belongs to.
	ReadsetId string `json:"readsetId,omitempty"`

	// ReferenceSequenceName: The name of the sequence that this read is
	// aligned to. This would be, for example, 'X' for the X Chromosome or
	// '20' for Chromosome 20. (RNAME)
	ReferenceSequenceName string `json:"referenceSequenceName,omitempty"`

	// Tags: A map of additional read information. (TAG)
	Tags map[string][]string `json:"tags,omitempty"`

	// TemplateLength: Length of the original piece of DNA that produced
	// both this read and the paired read. (TLEN)
	TemplateLength int64 `json:"templateLength,omitempty"`
}

type ReadGroup 

type ReadGroup struct {
	// Date: (DT) Date the run was produced (ISO8601 date or date/time).
	Date string `json:"date,omitempty"`

	// Description: (DS) Description.
	Description string `json:"description,omitempty"`

	// FlowOrder: (FO) Flow order. The array of nucleotide bases that
	// correspond to the nucleotides used for each flow of each read.
	FlowOrder string `json:"flowOrder,omitempty"`

	// Id: (ID) Read group identifier.
	Id string `json:"id,omitempty"`

	// KeySequence: (KS) The array of nucleotide bases that correspond to
	// the key sequence of each read.
	KeySequence string `json:"keySequence,omitempty"`

	// Library: (LS) Library.
	Library string `json:"library,omitempty"`

	// PlatformUnit: (PU) Platform unit.
	PlatformUnit string `json:"platformUnit,omitempty"`

	// PredictedInsertSize: (PI) Predicted median insert size.
	PredictedInsertSize int64 `json:"predictedInsertSize,omitempty"`

	// ProcessingProgram: (PG) Programs used for processing the read group.
	ProcessingProgram string `json:"processingProgram,omitempty"`

	// Sample: (SM) Sample.
	Sample string `json:"sample,omitempty"`

	// SequencingCenterName: (CN) Name of sequencing center producing the
	// read.
	SequencingCenterName string `json:"sequencingCenterName,omitempty"`

	// SequencingTechnology: (PL) Platform/technology used to produce the
	// reads.
	SequencingTechnology string `json:"sequencingTechnology,omitempty"`
}

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 readsets. Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested readsets 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 readset IDs yields all reads in those readsets, 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.

type Readset 

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

	// FileData: File information from the original BAM import. See the BAM
	// format specification for additional information on each field.
	FileData []*HeaderSection `json:"fileData,omitempty"`

	// Id: The Google generated ID of the readset, immutable.
	Id string `json:"id,omitempty"`

	// Name: The readset name, typically this is the sample name.
	Name string `json:"name,omitempty"`
}

type ReadsetsCoveragebucketsListCall 

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

func (*ReadsetsCoveragebucketsListCall) Do 

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

func (*ReadsetsCoveragebucketsListCall) Fields 

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

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

func (*ReadsetsCoveragebucketsListCall) MaxResults 

func (c *ReadsetsCoveragebucketsListCall) MaxResults(maxResults uint64) *ReadsetsCoveragebucketsListCall

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

func (*ReadsetsCoveragebucketsListCall) PageToken 

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

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 (*ReadsetsCoveragebucketsListCall) RangeSequenceEnd 

func (c *ReadsetsCoveragebucketsListCall) RangeSequenceEnd(rangeSequenceEnd uint64) *ReadsetsCoveragebucketsListCall

RangeSequenceEnd sets the optional parameter "range.sequenceEnd": The end position of the range on the reference, 1-based exclusive. If specified, sequenceName must also be specified.

func (*ReadsetsCoveragebucketsListCall) RangeSequenceName 

func (c *ReadsetsCoveragebucketsListCall) RangeSequenceName(rangeSequenceName string) *ReadsetsCoveragebucketsListCall

RangeSequenceName sets the optional parameter "range.sequenceName": The reference sequence name, for example chr1, 1, or chrX.

func (*ReadsetsCoveragebucketsListCall) RangeSequenceStart 

func (c *ReadsetsCoveragebucketsListCall) RangeSequenceStart(rangeSequenceStart uint64) *ReadsetsCoveragebucketsListCall

RangeSequenceStart sets the optional parameter "range.sequenceStart": The start position of the range on the reference, 1-based inclusive. If specified, sequenceName must also be specified.

func (*ReadsetsCoveragebucketsListCall) TargetBucketWidth 

func (c *ReadsetsCoveragebucketsListCall) TargetBucketWidth(targetBucketWidth uint64) *ReadsetsCoveragebucketsListCall

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 ReadsetsCoveragebucketsService 

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

func NewReadsetsCoveragebucketsService 

func NewReadsetsCoveragebucketsService(s *Service) *ReadsetsCoveragebucketsService

func (*ReadsetsCoveragebucketsService) List 

func (r *ReadsetsCoveragebucketsService) List(readsetId string) *ReadsetsCoveragebucketsListCall

List: Lists fixed width coverage buckets for a readset, 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 various bucket widths, enabling various coverage "zoom levels". The caller must have READ permissions for the target readset.

type ReadsetsDeleteCall 

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

func (*ReadsetsDeleteCall) Do 

func (c *ReadsetsDeleteCall) Do() error

func (*ReadsetsDeleteCall) Fields 

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

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

type ReadsetsExportCall 

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

func (*ReadsetsExportCall) Do 

func (c *ReadsetsExportCall) Do() (*ExportReadsetsResponse, error)

func (*ReadsetsExportCall) Fields 

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

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

type ReadsetsGetCall 

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

func (*ReadsetsGetCall) Do 

func (c *ReadsetsGetCall) Do() (*Readset, error)

func (*ReadsetsGetCall) Fields 

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

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

type ReadsetsImportCall 

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

func (*ReadsetsImportCall) Do 

func (c *ReadsetsImportCall) Do() (*ImportReadsetsResponse, error)

func (*ReadsetsImportCall) Fields 

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

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

type ReadsetsPatchCall 

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

func (*ReadsetsPatchCall) Do 

func (c *ReadsetsPatchCall) Do() (*Readset, error)

func (*ReadsetsPatchCall) Fields 

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

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

type ReadsetsSearchCall 

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

func (*ReadsetsSearchCall) Do 

func (c *ReadsetsSearchCall) Do() (*SearchReadsetsResponse, error)

func (*ReadsetsSearchCall) Fields 

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

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

type ReadsetsService 

type ReadsetsService struct {
	Coveragebuckets *ReadsetsCoveragebucketsService
	// contains filtered or unexported fields
}

func NewReadsetsService 

func NewReadsetsService(s *Service) *ReadsetsService

func (*ReadsetsService) Delete 

func (r *ReadsetsService) Delete(readsetId string) *ReadsetsDeleteCall

Delete: Deletes a readset.

func (*ReadsetsService) Export 

func (r *ReadsetsService) Export(exportreadsetsrequest *ExportReadsetsRequest) *ReadsetsExportCall

Export: Exports readsets 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, and some custom tags will be converted to strings.

func (*ReadsetsService) Get 

func (r *ReadsetsService) Get(readsetId string) *ReadsetsGetCall

Get: Gets a readset by ID.

func (*ReadsetsService) Import 

func (r *ReadsetsService) Import(importreadsetsrequest *ImportReadsetsRequest) *ReadsetsImportCall

Import: Creates readsets 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 (*ReadsetsService) Patch 

func (r *ReadsetsService) Patch(readsetId string, readset *Readset) *ReadsetsPatchCall

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

func (*ReadsetsService) Search 

func (r *ReadsetsService) Search(searchreadsetsrequest *SearchReadsetsRequest) *ReadsetsSearchCall

Search: Gets a list of readsets matching the criteria.

func (*ReadsetsService) Update 

func (r *ReadsetsService) Update(readsetId string, readset *Readset) *ReadsetsUpdateCall

Update: Updates a readset.

type ReadsetsUpdateCall 

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

func (*ReadsetsUpdateCall) Do 

func (c *ReadsetsUpdateCall) Do() (*Readset, error)

func (*ReadsetsUpdateCall) Fields 

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

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

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"`
}

type ReferenceSequence 

type ReferenceSequence struct {
	// AssemblyId: (AS) Genome assembly identifier.
	AssemblyId string `json:"assemblyId,omitempty"`

	// Length: (LN) Reference sequence length.
	Length int64 `json:"length,omitempty"`

	// Md5Checksum: (M5) MD5 checksum of the sequence in the uppercase,
	// excluding spaces but including pads as *.
	Md5Checksum string `json:"md5Checksum,omitempty"`

	// Name: (SN) Reference sequence name.
	Name string `json:"name,omitempty"`

	// Species: (SP) Species.
	Species string `json:"species,omitempty"`

	// Uri: (UR) URI of the sequence.
	Uri string `json:"uri,omitempty"`
}

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.
	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"`
}

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"`
}

type SearchJobsRequest 

type SearchJobsRequest struct {
	// CreatedAfter: If specified, only jobs created on or after this date,
	// given in milliseconds since Unix epoch, will be returned.
	CreatedAfter int64 `json:"createdAfter,omitempty,string"`

	// CreatedBefore: If specified, only jobs created prior to this date,
	// given in milliseconds since Unix epoch, will be returned.
	CreatedBefore int64 `json:"createdBefore,omitempty,string"`

	// MaxResults: Specifies the number of results to return in a single
	// page. Defaults to 128. The maximum value is 256.
	MaxResults uint64 `json:"maxResults,omitempty,string"`

	// 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 the nextPageToken from the previous response.
	PageToken string `json:"pageToken,omitempty"`

	// ProjectId: Required. Only return jobs which belong to this Google
	// Developers
	ProjectId int64 `json:"projectId,omitempty,string"`

	// Status: Only return jobs which have a matching status.
	Status []string `json:"status,omitempty"`
}

type SearchJobsResponse 

type SearchJobsResponse struct {
	// Jobs: The list of jobs results, ordered newest to oldest.
	Jobs []*Job `json:"jobs,omitempty"`

	// NextPageToken: The continuation token which is used to page through
	// large result sets. Provide this value is a subsequent request to
	// return the next page of results. This field will be empty if there
	// are no more results.
	NextPageToken string `json:"nextPageToken,omitempty"`
}

type SearchReadsRequest 

type SearchReadsRequest struct {
	// MaxResults: Specifies number of results to return in a single page.
	// If unspecified, it will default to 256. The maximum value is 2048.
	MaxResults uint64 `json:"maxResults,omitempty,string"`

	// 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"`

	// ReadsetIds: The readsets within which to search for reads. At least
	// one readset ID must be provided. All specified readsets must be
	// aligned against a common set of reference sequences; this defines the
	// genomic coordinates for the query.
	ReadsetIds []string `json:"readsetIds,omitempty"`

	// SequenceEnd: The end position (1-based, inclusive) of the target
	// range. If specified, sequenceName must also be specified. Defaults to
	// the end of the target reference sequence, if any.
	SequenceEnd uint64 `json:"sequenceEnd,omitempty,string"`

	// SequenceName: Restricts the results to a particular reference
	// sequence such as 1, chr1, or X. The set of valid references sequences
	// depends on the readsets specified. If set to *, only unmapped Reads
	// are returned.
	SequenceName string `json:"sequenceName,omitempty"`

	// SequenceStart: The start position (1-based, inclusive) of the target
	// range. If specified, sequenceName must also be specified. Defaults to
	// the start of the target reference sequence, if any.
	SequenceStart uint64 `json:"sequenceStart,omitempty,string"`
}

type SearchReadsResponse 

type SearchReadsResponse 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"`

	// Reads: The list of matching Reads. The resulting Reads are sorted by
	// position; the smallest positions are returned first. Unmapped reads,
	// which have no position, are returned last and are further sorted
	// alphabetically by name.
	Reads []*Read `json:"reads,omitempty"`
}

type SearchReadsetsRequest 

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

	// MaxResults: Specifies number of results to return in a single page.
	// If unspecified, it will default to 128. The maximum value is 1024.
	MaxResults uint64 `json:"maxResults,omitempty,string"`

	// Name: Only return readsets for which a substring of the name matches
	// this string.
	Name string `json:"name,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 SearchReadsetsResponse 

type SearchReadsetsResponse 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"`

	// Readsets: The list of matching Readsets.
	Readsets []*Readset `json:"readsets,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"`
}

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"`
}

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: Required. The end of the window (0-based, exclusive) for which
	// overlapping variants should be returned.
	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.
	MaxCalls int64 `json:"maxCalls,omitempty"`

	// PageSize: The maximum number of variants to return.
	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: Required. The beginning of the window (0-based, inclusive) for
	// which overlapping variants should be returned.
	Start int64 `json:"start,omitempty,string"`

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

	// VariantSetIds: Exactly one variant set ID must be provided. Only
	// variants from this variant set will be returned.
	VariantSetIds []string `json:"variantSetIds,omitempty"`
}

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"`
}

type Service 

type Service struct {
	BasePath string // API endpoint base URL

	Callsets *CallsetsService

	Datasets *DatasetsService

	Experimental *ExperimentalService

	Jobs *JobsService

	Reads *ReadsService

	Readsets *ReadsetsService

	Variants *VariantsService

	Variantsets *VariantsetsService
	// contains filtered or unexported fields
}

func New 

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

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 []*Call `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 Google generated ID of the variant, immutable.
	Id string `json:"id,omitempty"`

	// Info: A map of additional variant information.
	Info map[string][]string `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"`
}

type VariantSet 

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

	// Id: The Google-generated ID of the variant set. Immutable.
	Id string `json:"id,omitempty"`

	// Metadata: The metadata associated with this variant set.
	Metadata []*Metadata `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"`
}

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() 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 VariantsExportCall 

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

func (*VariantsExportCall) Do 

func (c *VariantsExportCall) Do() (*ExportVariantsResponse, error)

func (*VariantsExportCall) Fields 

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

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() (*ImportVariantsResponse, 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 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) Export 

func (r *VariantsService) Export(exportvariantsrequest *ExportVariantsRequest) *VariantsExportCall

Export: Exports variant data to an external destination.

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) Search 

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

Search: Gets a list of variants matching the criteria.

Implements GlobalAllianceApi.searchVariants.

func (*VariantsService) Update 

func (r *VariantsService) Update(variantId string, variant *Variant) *VariantsUpdateCall

Update: Updates a variant's names and info fields. All other modifications are silently ignored. Returns the modified variant without its calls.

type VariantsUpdateCall 

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

func (*VariantsUpdateCall) Do 

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

func (*VariantsUpdateCall) Fields 

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

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() 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 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 VariantsetsMergeVariantsCall 

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

func (*VariantsetsMergeVariantsCall) Do 

func (c *VariantsetsMergeVariantsCall) Do() error

func (*VariantsetsMergeVariantsCall) Fields 

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

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.

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) 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) Get 

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

Get: Gets a variant set by ID.

func (*VariantsetsService) MergeVariants 

func (r *VariantsetsService) MergeVariants(variantSetId string, mergevariantsrequest *MergeVariantsRequest) *VariantsetsMergeVariantsCall

MergeVariants: 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 (*VariantsetsService) Patch 

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

Patch: Updates a variant set's metadata. All other modifications are silently ignored. 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.

func (*VariantsetsService) Update 

func (r *VariantsetsService) Update(variantSetId string, variantset *VariantSet) *VariantsetsUpdateCall

Update: Updates a variant set's metadata. All other modifications are silently ignored.

type VariantsetsUpdateCall 

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

func (*VariantsetsUpdateCall) Do 

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

func (*VariantsetsUpdateCall) Fields 

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

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

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.