ActiveGo 1.8Package genomics
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Constants
OAuth2 scopes used by this API.
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"
)
type Annotation ¶
Annotation: An annotation describes a region of reference genome. The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. An annotation is not inherently associated with a specific sample or individual (though a client could choose to use annotations in this way). Example canonical annotation types are `GENE` and `VARIANT`.
type Annotation struct {
// AnnotationSetId: The annotation set to which this annotation belongs.
AnnotationSetId string `json:"annotationSetId,omitempty"`
// End: The end position of the range on the reference, 0-based
// exclusive.
End int64 `json:"end,omitempty,string"`
// Id: The server-generated annotation ID, unique across all
// annotations.
Id string `json:"id,omitempty"`
// Info: A map of additional read alignment information. This must be of
// the form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `json:"info,omitempty"`
// Name: The display name of this annotation.
Name string `json:"name,omitempty"`
// ReferenceId: The ID of the Google Genomics reference associated with
// this range.
ReferenceId string `json:"referenceId,omitempty"`
// ReferenceName: The display name corresponding to the reference
// specified by
// `referenceId`, for example `chr1`, `1`, or `chrX`.
ReferenceName string `json:"referenceName,omitempty"`
// ReverseStrand: Whether this range refers to the reverse strand, as
// opposed to the forward
// strand. Note that regardless of this field, the start/end position of
// the
// range always refer to the forward strand.
ReverseStrand bool `json:"reverseStrand,omitempty"`
// Start: The start position of the range on the reference, 0-based
// inclusive.
Start int64 `json:"start,omitempty,string"`
// Transcript: A transcript value represents the assertion that a
// particular region of
// the reference genome may be transcribed as RNA. An alternative
// splicing
// pattern would be represented as a separate transcript object. This
// field
// is only set for annotations of type `TRANSCRIPT`.
Transcript *Transcript `json:"transcript,omitempty"`
// Type: The data type for this annotation. Must match the containing
// annotation
// set's type.
//
// Possible values:
// "ANNOTATION_TYPE_UNSPECIFIED"
// "GENERIC" - A `GENERIC` annotation type should be used when no
// other annotation
// type will suffice. This represents an untyped annotation of the
// reference
// genome.
// "VARIANT" - A `VARIANT` annotation type.
// "GENE" - A `GENE` annotation type represents the existence of a
// gene at the
// associated reference coordinates. The start coordinate is typically
// the
// gene's transcription start site and the end is typically the end of
// the
// gene's last exon.
// "TRANSCRIPT" - A `TRANSCRIPT` annotation type represents the
// assertion that a
// particular region of the reference genome may be transcribed as RNA.
Type string `json:"type,omitempty"`
// Variant: A variant annotation, which describes the effect of a
// variant on the
// genome, the coding sequence, and/or higher level consequences at
// the
// organism level e.g. pathogenicity. This field is only set for
// annotations
// of type `VARIANT`.
Variant *VariantAnnotation `json:"variant,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "AnnotationSetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AnnotationSetId") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*Annotation) MarshalJSON ¶
func (s *Annotation) MarshalJSON() ([]byte, error)
type AnnotationSet ¶
AnnotationSet: An annotation set is a logical grouping of annotations that share consistent type information and provenance. Examples of annotation sets include 'all genes from refseq', and 'all variant annotations from ClinVar'.
type AnnotationSet struct {
// DatasetId: The dataset to which this annotation set belongs.
DatasetId string `json:"datasetId,omitempty"`
// Id: The server-generated annotation set ID, unique across all
// annotation sets.
Id string `json:"id,omitempty"`
// Info: A map of additional read alignment information. This must be of
// the form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `json:"info,omitempty"`
// Name: The display name for this annotation set.
Name string `json:"name,omitempty"`
// ReferenceSetId: The ID of the reference set that defines the
// coordinate space for this
// set's annotations.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// SourceUri: The source URI describing the file from which this
// annotation set was
// generated, if any.
SourceUri string `json:"sourceUri,omitempty"`
// Type: The type of annotations contained within this set.
//
// Possible values:
// "ANNOTATION_TYPE_UNSPECIFIED"
// "GENERIC" - A `GENERIC` annotation type should be used when no
// other annotation
// type will suffice. This represents an untyped annotation of the
// reference
// genome.
// "VARIANT" - A `VARIANT` annotation type.
// "GENE" - A `GENE` annotation type represents the existence of a
// gene at the
// associated reference coordinates. The start coordinate is typically
// the
// gene's transcription start site and the end is typically the end of
// the
// gene's last exon.
// "TRANSCRIPT" - A `TRANSCRIPT` annotation type represents the
// assertion that a
// particular region of the reference genome may be transcribed as RNA.
Type string `json:"type,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*AnnotationSet) MarshalJSON ¶
func (s *AnnotationSet) MarshalJSON() ([]byte, error)
type AnnotationsBatchCreateCall ¶
type AnnotationsBatchCreateCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsBatchCreateCall) Context ¶
func (c *AnnotationsBatchCreateCall) Context(ctx context.Context) *AnnotationsBatchCreateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsBatchCreateCall) Do ¶
func (c *AnnotationsBatchCreateCall) Do(opts ...googleapi.CallOption) (*BatchCreateAnnotationsResponse, error)
Do executes the "genomics.annotations.batchCreate" call. Exactly one of *BatchCreateAnnotationsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *BatchCreateAnnotationsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsBatchCreateCall) Fields ¶
func (c *AnnotationsBatchCreateCall) Fields(s ...googleapi.Field) *AnnotationsBatchCreateCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsBatchCreateCall) Header ¶
func (c *AnnotationsBatchCreateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type AnnotationsCreateCall ¶
type AnnotationsCreateCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsCreateCall) Context ¶
func (c *AnnotationsCreateCall) Context(ctx context.Context) *AnnotationsCreateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsCreateCall) Do ¶
func (c *AnnotationsCreateCall) Do(opts ...googleapi.CallOption) (*Annotation, error)
Do executes the "genomics.annotations.create" call. Exactly one of *Annotation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Annotation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsCreateCall) Fields ¶
func (c *AnnotationsCreateCall) Fields(s ...googleapi.Field) *AnnotationsCreateCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsCreateCall) Header ¶
func (c *AnnotationsCreateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type AnnotationsDeleteCall ¶
type AnnotationsDeleteCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsDeleteCall) Context ¶
func (c *AnnotationsDeleteCall) Context(ctx context.Context) *AnnotationsDeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsDeleteCall) Do ¶
func (c *AnnotationsDeleteCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.annotations.delete" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsDeleteCall) Fields ¶
func (c *AnnotationsDeleteCall) Fields(s ...googleapi.Field) *AnnotationsDeleteCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsDeleteCall) Header ¶
func (c *AnnotationsDeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type AnnotationsGetCall ¶
type AnnotationsGetCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsGetCall) Context ¶
func (c *AnnotationsGetCall) Context(ctx context.Context) *AnnotationsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsGetCall) Do ¶
func (c *AnnotationsGetCall) Do(opts ...googleapi.CallOption) (*Annotation, error)
Do executes the "genomics.annotations.get" call. Exactly one of *Annotation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Annotation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsGetCall) Fields ¶
func (c *AnnotationsGetCall) Fields(s ...googleapi.Field) *AnnotationsGetCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsGetCall) Header ¶
func (c *AnnotationsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*AnnotationsGetCall) IfNoneMatch ¶
func (c *AnnotationsGetCall) IfNoneMatch(entityTag string) *AnnotationsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type AnnotationsSearchCall ¶
type AnnotationsSearchCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsSearchCall) Context ¶
func (c *AnnotationsSearchCall) Context(ctx context.Context) *AnnotationsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsSearchCall) Do ¶
func (c *AnnotationsSearchCall) Do(opts ...googleapi.CallOption) (*SearchAnnotationsResponse, error)
Do executes the "genomics.annotations.search" call. Exactly one of *SearchAnnotationsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchAnnotationsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsSearchCall) Fields ¶
func (c *AnnotationsSearchCall) Fields(s ...googleapi.Field) *AnnotationsSearchCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsSearchCall) Header ¶
func (c *AnnotationsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*AnnotationsSearchCall) Pages ¶
func (c *AnnotationsSearchCall) Pages(ctx context.Context, f func(*SearchAnnotationsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
type AnnotationsService ¶
type AnnotationsService struct {
// contains filtered or unexported fields
}
func NewAnnotationsService ¶
func NewAnnotationsService(s *Service) *AnnotationsService
func (*AnnotationsService) BatchCreate ¶
func (r *AnnotationsService) BatchCreate(batchcreateannotationsrequest *BatchCreateAnnotationsRequest) *AnnotationsBatchCreateCall
BatchCreate: Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together.
If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally.
For details on the requirements for each individual annotation resource, see CreateAnnotation.
func (*AnnotationsService) Create ¶
func (r *AnnotationsService) Create(annotation *Annotation) *AnnotationsCreateCall
Create: Creates a new annotation. Caller must have WRITE permission for the associated annotation set.
The following fields are required:
* annotationSetId * referenceName or
referenceId
### Transcripts
For annotations of type TRANSCRIPT, the following fields of transcript must be provided:
* exons.start * exons.end
All other fields may be optionally specified, unless documented as being server-generated (for example, the `id` field). The annotated range must be no longer than 100Mbp (mega base pairs). See the Annotation resource for additional restrictions on each field.
func (*AnnotationsService) Delete ¶
func (r *AnnotationsService) Delete(annotationId string) *AnnotationsDeleteCall
Delete: Deletes an annotation. Caller must have WRITE permission for the associated annotation set.
func (*AnnotationsService) Get ¶
func (r *AnnotationsService) Get(annotationId string) *AnnotationsGetCall
Get: Gets an annotation. Caller must have READ permission for the associated annotation set.
func (*AnnotationsService) Search ¶
func (r *AnnotationsService) Search(searchannotationsrequest *SearchAnnotationsRequest) *AnnotationsSearchCall
Search: Searches for annotations that match the given criteria. Results are ordered by genomic coordinate (by reference sequence, then position). Annotations with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotations in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried annotation sets.
func (*AnnotationsService) Update ¶
func (r *AnnotationsService) Update(annotationId string, annotation *Annotation) *AnnotationsUpdateCall
Update: Updates an annotation. Caller must have WRITE permission for the associated dataset.
type AnnotationsUpdateCall ¶
type AnnotationsUpdateCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsUpdateCall) Context ¶
func (c *AnnotationsUpdateCall) Context(ctx context.Context) *AnnotationsUpdateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsUpdateCall) Do ¶
func (c *AnnotationsUpdateCall) Do(opts ...googleapi.CallOption) (*Annotation, error)
Do executes the "genomics.annotations.update" call. Exactly one of *Annotation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Annotation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsUpdateCall) Fields ¶
func (c *AnnotationsUpdateCall) Fields(s ...googleapi.Field) *AnnotationsUpdateCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsUpdateCall) Header ¶
func (c *AnnotationsUpdateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*AnnotationsUpdateCall) UpdateMask ¶
func (c *AnnotationsUpdateCall) UpdateMask(updateMask string) *AnnotationsUpdateCall
UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. Mutable fields are name, variant, transcript, and info. If unspecified, all mutable fields will be updated.
type AnnotationsetsCreateCall ¶
type AnnotationsetsCreateCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsetsCreateCall) Context ¶
func (c *AnnotationsetsCreateCall) Context(ctx context.Context) *AnnotationsetsCreateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsetsCreateCall) Do ¶
func (c *AnnotationsetsCreateCall) Do(opts ...googleapi.CallOption) (*AnnotationSet, error)
Do executes the "genomics.annotationsets.create" call. Exactly one of *AnnotationSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *AnnotationSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsetsCreateCall) Fields ¶
func (c *AnnotationsetsCreateCall) Fields(s ...googleapi.Field) *AnnotationsetsCreateCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsetsCreateCall) Header ¶
func (c *AnnotationsetsCreateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type AnnotationsetsDeleteCall ¶
type AnnotationsetsDeleteCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsetsDeleteCall) Context ¶
func (c *AnnotationsetsDeleteCall) Context(ctx context.Context) *AnnotationsetsDeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsetsDeleteCall) Do ¶
func (c *AnnotationsetsDeleteCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.annotationsets.delete" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsetsDeleteCall) Fields ¶
func (c *AnnotationsetsDeleteCall) Fields(s ...googleapi.Field) *AnnotationsetsDeleteCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsetsDeleteCall) Header ¶
func (c *AnnotationsetsDeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type AnnotationsetsGetCall ¶
type AnnotationsetsGetCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsetsGetCall) Context ¶
func (c *AnnotationsetsGetCall) Context(ctx context.Context) *AnnotationsetsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsetsGetCall) Do ¶
func (c *AnnotationsetsGetCall) Do(opts ...googleapi.CallOption) (*AnnotationSet, error)
Do executes the "genomics.annotationsets.get" call. Exactly one of *AnnotationSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *AnnotationSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsetsGetCall) Fields ¶
func (c *AnnotationsetsGetCall) Fields(s ...googleapi.Field) *AnnotationsetsGetCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsetsGetCall) Header ¶
func (c *AnnotationsetsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*AnnotationsetsGetCall) IfNoneMatch ¶
func (c *AnnotationsetsGetCall) IfNoneMatch(entityTag string) *AnnotationsetsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type AnnotationsetsSearchCall ¶
type AnnotationsetsSearchCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsetsSearchCall) Context ¶
func (c *AnnotationsetsSearchCall) Context(ctx context.Context) *AnnotationsetsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsetsSearchCall) Do ¶
func (c *AnnotationsetsSearchCall) Do(opts ...googleapi.CallOption) (*SearchAnnotationSetsResponse, error)
Do executes the "genomics.annotationsets.search" call. Exactly one of *SearchAnnotationSetsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchAnnotationSetsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsetsSearchCall) Fields ¶
func (c *AnnotationsetsSearchCall) Fields(s ...googleapi.Field) *AnnotationsetsSearchCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsetsSearchCall) Header ¶
func (c *AnnotationsetsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*AnnotationsetsSearchCall) Pages ¶
func (c *AnnotationsetsSearchCall) Pages(ctx context.Context, f func(*SearchAnnotationSetsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
type AnnotationsetsService ¶
type AnnotationsetsService struct {
// contains filtered or unexported fields
}
func NewAnnotationsetsService ¶
func NewAnnotationsetsService(s *Service) *AnnotationsetsService
func (*AnnotationsetsService) Create ¶
func (r *AnnotationsetsService) Create(annotationset *AnnotationSet) *AnnotationsetsCreateCall
Create: Creates a new annotation set. Caller must have WRITE permission for the associated dataset.
The following fields are required:
* datasetId * referenceSetId
All other fields may be optionally specified, unless documented as being server-generated (for example, the `id` field).
func (*AnnotationsetsService) Delete ¶
func (r *AnnotationsetsService) Delete(annotationSetId string) *AnnotationsetsDeleteCall
Delete: Deletes an annotation set. Caller must have WRITE permission for the associated annotation set.
func (*AnnotationsetsService) Get ¶
func (r *AnnotationsetsService) Get(annotationSetId string) *AnnotationsetsGetCall
Get: Gets an annotation set. Caller must have READ permission for the associated dataset.
func (*AnnotationsetsService) Search ¶
func (r *AnnotationsetsService) Search(searchannotationsetsrequest *SearchAnnotationSetsRequest) *AnnotationsetsSearchCall
Search: Searches for annotation sets that match the given criteria. Annotation sets are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotation sets in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried datasets.
func (*AnnotationsetsService) Update ¶
func (r *AnnotationsetsService) Update(annotationSetId string, annotationset *AnnotationSet) *AnnotationsetsUpdateCall
Update: Updates an annotation set. The update must respect all mutability restrictions and other invariants described on the annotation set resource. Caller must have WRITE permission for the associated dataset.
type AnnotationsetsUpdateCall ¶
type AnnotationsetsUpdateCall struct {
// contains filtered or unexported fields
}
func (*AnnotationsetsUpdateCall) Context ¶
func (c *AnnotationsetsUpdateCall) Context(ctx context.Context) *AnnotationsetsUpdateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*AnnotationsetsUpdateCall) Do ¶
func (c *AnnotationsetsUpdateCall) Do(opts ...googleapi.CallOption) (*AnnotationSet, error)
Do executes the "genomics.annotationsets.update" call. Exactly one of *AnnotationSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *AnnotationSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*AnnotationsetsUpdateCall) Fields ¶
func (c *AnnotationsetsUpdateCall) Fields(s ...googleapi.Field) *AnnotationsetsUpdateCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*AnnotationsetsUpdateCall) Header ¶
func (c *AnnotationsetsUpdateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*AnnotationsetsUpdateCall) UpdateMask ¶
func (c *AnnotationsetsUpdateCall) UpdateMask(updateMask string) *AnnotationsetsUpdateCall
UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. Mutable fields are name, source_uri, and info. If unspecified, all mutable fields will be updated.
type BatchCreateAnnotationsRequest ¶
type BatchCreateAnnotationsRequest struct {
// Annotations: The annotations to be created. At most 4096 can be
// specified in a single
// request.
Annotations []*Annotation `json:"annotations,omitempty"`
// RequestId: A unique request ID which enables the server to detect
// duplicated requests.
// If provided, duplicated requests will result in the same response; if
// not
// provided, duplicated requests may result in duplicated data. For a
// given
// annotation set, callers should not reuse `request_id`s when
// writing
// different batches of annotations - behavior in this case is
// undefined.
// A common approach is to use a UUID. For batch jobs where worker
// crashes are
// a possibility, consider using some unique variant of a worker or run
// ID.
RequestId string `json:"requestId,omitempty"`
// ForceSendFields is a list of field names (e.g. "Annotations") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Annotations") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*BatchCreateAnnotationsRequest) MarshalJSON ¶
func (s *BatchCreateAnnotationsRequest) MarshalJSON() ([]byte, error)
type BatchCreateAnnotationsResponse ¶
type BatchCreateAnnotationsResponse struct {
// Entries: The resulting per-annotation entries, ordered consistently
// with the
// original request.
Entries []*Entry `json:"entries,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Entries") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Entries") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*BatchCreateAnnotationsResponse) MarshalJSON ¶
func (s *BatchCreateAnnotationsResponse) MarshalJSON() ([]byte, error)
type Binding ¶
Binding: Associates `members` with a `role`.
type Binding struct {
// Members: Specifies the identities requesting access for a Cloud
// Platform resource.
// `members` can have the following values:
//
// * `allUsers`: A special identifier that represents anyone who is
// on the internet; with or without a Google account.
//
// * `allAuthenticatedUsers`: A special identifier that represents
// anyone
// who is authenticated with a Google account or a service
// account.
//
// * `user:{emailid}`: An email address that represents a specific
// Google
// account. For example, `alice@gmail.com` or `joe@example.com`.
//
//
// * `serviceAccount:{emailid}`: An email address that represents a
// service
// account. For example,
// `my-other-app@appspot.gserviceaccount.com`.
//
// * `group:{emailid}`: An email address that represents a Google
// group.
// For example, `admins@example.com`.
//
//
// * `domain:{domain}`: A Google Apps domain name that represents all
// the
// users of that domain. For example, `google.com` or
// `example.com`.
//
//
Members []string `json:"members,omitempty"`
// Role: Role that is assigned to `members`.
// For example, `roles/viewer`, `roles/editor`, or
// `roles/owner`.
// Required
Role string `json:"role,omitempty"`
// ForceSendFields is a list of field names (e.g. "Members") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Members") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Binding) MarshalJSON ¶
func (s *Binding) MarshalJSON() ([]byte, error)
type CallSet ¶
CallSet: A call set is a collection of variant calls, typically for one sample. It belongs to a variant set.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `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.
// This field must
// have exactly length one, as a call set belongs to a single variant
// set.
// This field is repeated for compatibility with the
// [GA4GH
// 0.5.1
// API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resou
// rces/avro/variants.avdl#L76).
VariantSetIds []string `json:"variantSetIds,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Created") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Created") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*CallSet) MarshalJSON ¶
func (s *CallSet) MarshalJSON() ([]byte, error)
type CallsetsCreateCall ¶
type CallsetsCreateCall struct {
// contains filtered or unexported fields
}
func (*CallsetsCreateCall) Context ¶
func (c *CallsetsCreateCall) Context(ctx context.Context) *CallsetsCreateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*CallsetsCreateCall) Do ¶
func (c *CallsetsCreateCall) Do(opts ...googleapi.CallOption) (*CallSet, error)
Do executes the "genomics.callsets.create" call. Exactly one of *CallSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *CallSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*CallsetsCreateCall) Header ¶
func (c *CallsetsCreateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type CallsetsDeleteCall ¶
type CallsetsDeleteCall struct {
// contains filtered or unexported fields
}
func (*CallsetsDeleteCall) Context ¶
func (c *CallsetsDeleteCall) Context(ctx context.Context) *CallsetsDeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*CallsetsDeleteCall) Do ¶
func (c *CallsetsDeleteCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.callsets.delete" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*CallsetsDeleteCall) Header ¶
func (c *CallsetsDeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type CallsetsGetCall ¶
type CallsetsGetCall struct {
// contains filtered or unexported fields
}
func (*CallsetsGetCall) Context ¶
func (c *CallsetsGetCall) Context(ctx context.Context) *CallsetsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*CallsetsGetCall) Do ¶
func (c *CallsetsGetCall) Do(opts ...googleapi.CallOption) (*CallSet, error)
Do executes the "genomics.callsets.get" call. Exactly one of *CallSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *CallSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*CallsetsGetCall) Header ¶
func (c *CallsetsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*CallsetsGetCall) IfNoneMatch ¶
func (c *CallsetsGetCall) IfNoneMatch(entityTag string) *CallsetsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type CallsetsPatchCall ¶
type CallsetsPatchCall struct {
// contains filtered or unexported fields
}
func (*CallsetsPatchCall) Context ¶
func (c *CallsetsPatchCall) Context(ctx context.Context) *CallsetsPatchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*CallsetsPatchCall) Do ¶
func (c *CallsetsPatchCall) Do(opts ...googleapi.CallOption) (*CallSet, error)
Do executes the "genomics.callsets.patch" call. Exactly one of *CallSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *CallSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *CallsetsPatchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
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. 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) Context ¶
func (c *CallsetsSearchCall) Context(ctx context.Context) *CallsetsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*CallsetsSearchCall) Do ¶
func (c *CallsetsSearchCall) Do(opts ...googleapi.CallOption) (*SearchCallSetsResponse, error)
Do executes the "genomics.callsets.search" call. Exactly one of *SearchCallSetsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchCallSetsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*CallsetsSearchCall) Header ¶
func (c *CallsetsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*CallsetsSearchCall) Pages ¶
func (c *CallsetsSearchCall) Pages(ctx context.Context, f func(*SearchCallSetsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*CallsetsService) Delete ¶
func (r *CallsetsService) Delete(callSetId string) *CallsetsDeleteCall
Delete: Deletes a call set.
For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*CallsetsService) Get ¶
func (r *CallsetsService) Get(callSetId string) *CallsetsGetCall
Get: Gets a call set by ID.
For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*CallsetsService) Patch ¶
func (r *CallsetsService) Patch(callSetId string, callset *CallSet) *CallsetsPatchCall
Patch: Updates a call set.
For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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.
For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.searchCallSets](https://g ithub.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmet hods.avdl#L178).
type CancelOperationRequest ¶
CancelOperationRequest: The request message for Operations.CancelOperation.
type CancelOperationRequest struct {
}
type CigarUnit ¶
CigarUnit: A single CIGAR operation.
type CigarUnit struct {
// Possible values:
// "OPERATION_UNSPECIFIED"
// "ALIGNMENT_MATCH" - An alignment match indicates that a sequence
// can be aligned to the
// reference without evidence of an INDEL. Unlike the
// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
// the `ALIGNMENT_MATCH` operator does not indicate whether
// the
// reference and read sequences are an exact match. This operator
// is
// equivalent to SAM's `M`.
// "INSERT" - The insert operator indicates that the read contains
// evidence of bases
// being inserted into the reference. This operator is equivalent to
// SAM's
// `I`.
// "DELETE" - The delete operator indicates that the read contains
// evidence of bases
// being deleted from the reference. This operator is equivalent to
// SAM's
// `D`.
// "SKIP" - The skip operator indicates that this read skips a long
// segment of the
// reference, but the bases have not been deleted. This operator is
// commonly
// used when working with RNA-seq data, where reads may skip long
// segments
// of the reference between exons. This operator is equivalent to
// SAM's
// `N`.
// "CLIP_SOFT" - The soft clip operator indicates that bases at the
// start/end of a read
// have not been considered during alignment. This may occur if the
// majority
// of a read maps, except for low quality bases at the start/end of a
// read.
// This operator is equivalent to SAM's `S`. Bases that are soft
// clipped will still be stored in the read.
// "CLIP_HARD" - The hard clip operator indicates that bases at the
// start/end of a read
// have been omitted from this alignment. This may occur if this
// linear
// alignment is part of a chimeric alignment, or if the read has
// been
// trimmed (for example, during error correction or to trim poly-A tails
// for
// RNA-seq). This operator is equivalent to SAM's `H`.
// "PAD" - The pad operator indicates that there is padding in an
// alignment. This
// operator is equivalent to SAM's `P`.
// "SEQUENCE_MATCH" - This operator indicates that this portion of the
// aligned sequence exactly
// matches the reference. This operator is equivalent to SAM's `=`.
// "SEQUENCE_MISMATCH" - This operator indicates that this portion of
// the aligned sequence is an
// alignment match to the reference, but a sequence mismatch. This
// can
// indicate a SNP or a read error. This operator is equivalent to
// SAM's
// `X`.
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"`
// ForceSendFields is a list of field names (e.g. "Operation") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Operation") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*CigarUnit) MarshalJSON ¶
func (s *CigarUnit) MarshalJSON() ([]byte, error)
type ClinicalCondition ¶
type ClinicalCondition struct {
// ConceptId: The MedGen concept id associated with this gene.
// Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
ConceptId string `json:"conceptId,omitempty"`
// ExternalIds: The set of external IDs for this condition.
ExternalIds []*ExternalId `json:"externalIds,omitempty"`
// Names: A set of names for the condition.
Names []string `json:"names,omitempty"`
// OmimId: The OMIM id for this condition.
// Search for these IDs at http://omim.org/
OmimId string `json:"omimId,omitempty"`
// ForceSendFields is a list of field names (e.g. "ConceptId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ConceptId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ClinicalCondition) MarshalJSON ¶
func (s *ClinicalCondition) MarshalJSON() ([]byte, error)
type CodingSequence ¶
type CodingSequence struct {
// End: The end of the coding sequence on this annotation's reference
// sequence,
// 0-based exclusive. Note that this position is relative to the
// reference
// start, and *not* the containing annotation start.
End int64 `json:"end,omitempty,string"`
// Start: The start of the coding sequence on this annotation's
// reference sequence,
// 0-based inclusive. Note that this position is relative to the
// reference
// start, and *not* the containing annotation start.
Start int64 `json:"start,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "End") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "End") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*CodingSequence) MarshalJSON ¶
func (s *CodingSequence) MarshalJSON() ([]byte, error)
type ComputeEngine ¶
ComputeEngine: Describes a Compute Engine resource that is being managed by a running pipeline.
type ComputeEngine struct {
// DiskNames: The names of the disks that were created for this
// pipeline.
DiskNames []string `json:"diskNames,omitempty"`
// InstanceName: The instance on which the operation is running.
InstanceName string `json:"instanceName,omitempty"`
// MachineType: The machine type of the instance.
MachineType string `json:"machineType,omitempty"`
// Zone: The availability zone in which the instance resides.
Zone string `json:"zone,omitempty"`
// ForceSendFields is a list of field names (e.g. "DiskNames") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DiskNames") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ComputeEngine) MarshalJSON ¶
func (s *ComputeEngine) MarshalJSON() ([]byte, error)
type CoverageBucket ¶
CoverageBucket: A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.
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"`
// ForceSendFields is a list of field names (e.g. "MeanCoverage") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "MeanCoverage") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*CoverageBucket) MarshalJSON ¶
func (s *CoverageBucket) MarshalJSON() ([]byte, error)
func (*CoverageBucket) UnmarshalJSON ¶
func (s *CoverageBucket) UnmarshalJSON(data []byte) error
type Dataset ¶
Dataset: A Dataset is a collection of genomic data.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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 Cloud project ID that this dataset belongs to.
ProjectId string `json:"projectId,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "CreateTime") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CreateTime") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Dataset) MarshalJSON ¶
func (s *Dataset) MarshalJSON() ([]byte, error)
type DatasetsCreateCall ¶
type DatasetsCreateCall struct {
// contains filtered or unexported fields
}
func (*DatasetsCreateCall) Context ¶
func (c *DatasetsCreateCall) Context(ctx context.Context) *DatasetsCreateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsCreateCall) Do ¶
func (c *DatasetsCreateCall) Do(opts ...googleapi.CallOption) (*Dataset, error)
Do executes the "genomics.datasets.create" call. Exactly one of *Dataset or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Dataset.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*DatasetsCreateCall) Header ¶
func (c *DatasetsCreateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type DatasetsDeleteCall ¶
type DatasetsDeleteCall struct {
// contains filtered or unexported fields
}
func (*DatasetsDeleteCall) Context ¶
func (c *DatasetsDeleteCall) Context(ctx context.Context) *DatasetsDeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsDeleteCall) Do ¶
func (c *DatasetsDeleteCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.datasets.delete" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*DatasetsDeleteCall) Header ¶
func (c *DatasetsDeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type DatasetsGetCall ¶
type DatasetsGetCall struct {
// contains filtered or unexported fields
}
func (*DatasetsGetCall) Context ¶
func (c *DatasetsGetCall) Context(ctx context.Context) *DatasetsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsGetCall) Do ¶
func (c *DatasetsGetCall) Do(opts ...googleapi.CallOption) (*Dataset, error)
Do executes the "genomics.datasets.get" call. Exactly one of *Dataset or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Dataset.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*DatasetsGetCall) Header ¶
func (c *DatasetsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*DatasetsGetCall) IfNoneMatch ¶
func (c *DatasetsGetCall) IfNoneMatch(entityTag string) *DatasetsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type DatasetsGetIamPolicyCall ¶
type DatasetsGetIamPolicyCall struct {
// contains filtered or unexported fields
}
func (*DatasetsGetIamPolicyCall) Context ¶
func (c *DatasetsGetIamPolicyCall) Context(ctx context.Context) *DatasetsGetIamPolicyCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsGetIamPolicyCall) Do ¶
func (c *DatasetsGetIamPolicyCall) Do(opts ...googleapi.CallOption) (*Policy, error)
Do executes the "genomics.datasets.getIamPolicy" call. Exactly one of *Policy or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Policy.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*DatasetsGetIamPolicyCall) Fields ¶
func (c *DatasetsGetIamPolicyCall) Fields(s ...googleapi.Field) *DatasetsGetIamPolicyCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*DatasetsGetIamPolicyCall) Header ¶
func (c *DatasetsGetIamPolicyCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type DatasetsListCall ¶
type DatasetsListCall struct {
// contains filtered or unexported fields
}
func (*DatasetsListCall) Context ¶
func (c *DatasetsListCall) Context(ctx context.Context) *DatasetsListCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsListCall) Do ¶
func (c *DatasetsListCall) Do(opts ...googleapi.CallOption) (*ListDatasetsResponse, error)
Do executes the "genomics.datasets.list" call. Exactly one of *ListDatasetsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *ListDatasetsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *DatasetsListCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*DatasetsListCall) IfNoneMatch ¶
func (c *DatasetsListCall) IfNoneMatch(entityTag string) *DatasetsListCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
func (*DatasetsListCall) PageSize ¶
func (c *DatasetsListCall) PageSize(pageSize int64) *DatasetsListCall
PageSize sets the optional parameter "pageSize": The maximum number of results to return in a single page. 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) Pages ¶
func (c *DatasetsListCall) Pages(ctx context.Context, f func(*ListDatasetsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
func (*DatasetsListCall) ProjectId ¶
func (c *DatasetsListCall) ProjectId(projectId string) *DatasetsListCall
ProjectId sets the optional parameter "projectId": Required. The Google Cloud project ID to list datasets for.
type DatasetsPatchCall ¶
type DatasetsPatchCall struct {
// contains filtered or unexported fields
}
func (*DatasetsPatchCall) Context ¶
func (c *DatasetsPatchCall) Context(ctx context.Context) *DatasetsPatchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsPatchCall) Do ¶
func (c *DatasetsPatchCall) Do(opts ...googleapi.CallOption) (*Dataset, error)
Do executes the "genomics.datasets.patch" call. Exactly one of *Dataset or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Dataset.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *DatasetsPatchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
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. 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.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*DatasetsService) Delete ¶
func (r *DatasetsService) Delete(datasetId string) *DatasetsDeleteCall
Delete: Deletes a dataset and all of its contents (all read group sets, reference sets, variant sets, call sets, annotation sets, etc.) This is reversible (up to one week after the deletion) via the datasets.undelete operation.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*DatasetsService) Get ¶
func (r *DatasetsService) Get(datasetId string) *DatasetsGetCall
Get: Gets a dataset by ID.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*DatasetsService) GetIamPolicy ¶
func (r *DatasetsService) GetIamPolicy(resource string, getiampolicyrequest *GetIamPolicyRequest) *DatasetsGetIamPolicyCall
GetIamPolicy: Gets the access control policy for the dataset. This is empty if the policy or resource does not exist.
See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a Policy</a> for more information.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*DatasetsService) List ¶
func (r *DatasetsService) List() *DatasetsListCall
List: Lists datasets within a project.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*DatasetsService) Patch ¶
func (r *DatasetsService) Patch(datasetId string, dataset *Dataset) *DatasetsPatchCall
Patch: Updates a dataset.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
This method supports patch semantics.
func (*DatasetsService) SetIamPolicy ¶
func (r *DatasetsService) SetIamPolicy(resource string, setiampolicyrequest *SetIamPolicyRequest) *DatasetsSetIamPolicyCall
SetIamPolicy: Sets the access control policy on the specified dataset. Replaces any existing policy.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a Policy</a> for more information.
func (*DatasetsService) TestIamPermissions ¶
func (r *DatasetsService) TestIamPermissions(resource string, testiampermissionsrequest *TestIamPermissionsRequest) *DatasetsTestIamPermissionsCall
TestIamPermissions: Returns permissions that a caller has on the specified resource. See <a href="/iam/docs/managing-policies#testing_permissions">Testing Permiss ions</a> for more information.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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.
For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
This operation is only possible for a week after the deletion occurred.
type DatasetsSetIamPolicyCall ¶
type DatasetsSetIamPolicyCall struct {
// contains filtered or unexported fields
}
func (*DatasetsSetIamPolicyCall) Context ¶
func (c *DatasetsSetIamPolicyCall) Context(ctx context.Context) *DatasetsSetIamPolicyCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsSetIamPolicyCall) Do ¶
func (c *DatasetsSetIamPolicyCall) Do(opts ...googleapi.CallOption) (*Policy, error)
Do executes the "genomics.datasets.setIamPolicy" call. Exactly one of *Policy or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Policy.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*DatasetsSetIamPolicyCall) Fields ¶
func (c *DatasetsSetIamPolicyCall) Fields(s ...googleapi.Field) *DatasetsSetIamPolicyCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*DatasetsSetIamPolicyCall) Header ¶
func (c *DatasetsSetIamPolicyCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type DatasetsTestIamPermissionsCall ¶
type DatasetsTestIamPermissionsCall struct {
// contains filtered or unexported fields
}
func (*DatasetsTestIamPermissionsCall) Context ¶
func (c *DatasetsTestIamPermissionsCall) Context(ctx context.Context) *DatasetsTestIamPermissionsCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsTestIamPermissionsCall) Do ¶
func (c *DatasetsTestIamPermissionsCall) Do(opts ...googleapi.CallOption) (*TestIamPermissionsResponse, error)
Do executes the "genomics.datasets.testIamPermissions" call. Exactly one of *TestIamPermissionsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *TestIamPermissionsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
func (*DatasetsTestIamPermissionsCall) Fields ¶
func (c *DatasetsTestIamPermissionsCall) Fields(s ...googleapi.Field) *DatasetsTestIamPermissionsCall
Fields allows partial responses to be retrieved. See https://developers.google.com/gdata/docs/2.0/basics#PartialResponse for more information.
func (*DatasetsTestIamPermissionsCall) Header ¶
func (c *DatasetsTestIamPermissionsCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type DatasetsUndeleteCall ¶
type DatasetsUndeleteCall struct {
// contains filtered or unexported fields
}
func (*DatasetsUndeleteCall) Context ¶
func (c *DatasetsUndeleteCall) Context(ctx context.Context) *DatasetsUndeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*DatasetsUndeleteCall) Do ¶
func (c *DatasetsUndeleteCall) Do(opts ...googleapi.CallOption) (*Dataset, error)
Do executes the "genomics.datasets.undelete" call. Exactly one of *Dataset or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Dataset.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*DatasetsUndeleteCall) Header ¶
func (c *DatasetsUndeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type Empty ¶
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 Empty struct {
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
}
type Entry ¶
type Entry struct {
// Annotation: The created annotation, if creation was successful.
Annotation *Annotation `json:"annotation,omitempty"`
// Status: The creation status.
Status *Status `json:"status,omitempty"`
// ForceSendFields is a list of field names (e.g. "Annotation") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Annotation") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Entry) MarshalJSON ¶
func (s *Entry) MarshalJSON() ([]byte, error)
type Exon ¶
type Exon struct {
// End: The end position of the exon on this annotation's reference
// sequence,
// 0-based exclusive. Note that this is relative to the reference start,
// and
// *not* the containing annotation start.
End int64 `json:"end,omitempty,string"`
// Frame: The frame of this exon. Contains a value of 0, 1, or 2, which
// indicates
// the offset of the first coding base of the exon within the reading
// frame
// of the coding DNA sequence, if any. This field is dependent on
// the
// strandedness of this annotation (see
// Annotation.reverse_strand).
// For forward stranded annotations, this offset is relative to
// the
// exon.start. For reverse
// strand annotations, this offset is relative to the
// exon.end `- 1`.
//
// Unset if this exon does not intersect the coding sequence. Upon
// creation
// of a transcript, the frame must be populated for all or none of
// the
// coding exons.
Frame int64 `json:"frame,omitempty"`
// Start: The start position of the exon on this annotation's reference
// sequence,
// 0-based inclusive. Note that this is relative to the reference start,
// and
// **not** the containing annotation start.
Start int64 `json:"start,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "End") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "End") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Exon) MarshalJSON ¶
func (s *Exon) MarshalJSON() ([]byte, error)
type Experiment ¶
type Experiment struct {
// InstrumentModel: The instrument model used as part of this
// experiment. This maps to
// sequencing technology in the SAM spec.
InstrumentModel string `json:"instrumentModel,omitempty"`
// LibraryId: A client-supplied library identifier; a library is a
// collection of DNA
// fragments which have been prepared for sequencing from a sample.
// This
// field is important for quality control as error or bias can be
// introduced
// during sample preparation.
LibraryId string `json:"libraryId,omitempty"`
// PlatformUnit: The platform unit used as part of this experiment, for
// example
// flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to
// the
// @RG PU field in the SAM spec.
PlatformUnit string `json:"platformUnit,omitempty"`
// SequencingCenter: The sequencing center used as part of this
// experiment.
SequencingCenter string `json:"sequencingCenter,omitempty"`
// ForceSendFields is a list of field names (e.g. "InstrumentModel") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "InstrumentModel") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*Experiment) MarshalJSON ¶
func (s *Experiment) MarshalJSON() ([]byte, error)
type ExportReadGroupSetRequest ¶
ExportReadGroupSetRequest: The read group set export request.
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 Cloud project ID that owns
// this
// export. The caller must have WRITE access to this project.
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"`
// ForceSendFields is a list of field names (e.g. "ExportUri") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ExportUri") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ExportReadGroupSetRequest) MarshalJSON ¶
func (s *ExportReadGroupSetRequest) MarshalJSON() ([]byte, error)
type ExportVariantSetRequest ¶
ExportVariantSetRequest: The variant data export request.
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" - Export the data to Google 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"`
// ForceSendFields is a list of field names (e.g. "BigqueryDataset") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "BigqueryDataset") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*ExportVariantSetRequest) MarshalJSON ¶
func (s *ExportVariantSetRequest) MarshalJSON() ([]byte, error)
type ExternalId ¶
type ExternalId struct {
// Id: The id used by the source of this data.
Id string `json:"id,omitempty"`
// SourceName: The name of the source of this data.
SourceName string `json:"sourceName,omitempty"`
// ForceSendFields is a list of field names (e.g. "Id") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Id") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ExternalId) MarshalJSON ¶
func (s *ExternalId) MarshalJSON() ([]byte, error)
type GetIamPolicyRequest ¶
GetIamPolicyRequest: Request message for `GetIamPolicy` method.
type GetIamPolicyRequest struct {
}
type ImportReadGroupSetsRequest ¶
ImportReadGroupSetsRequest: The read group set import request.
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" - In most cases, this strategy yields one
// read group set per file. This is
// the default behavior.
//
// Allocate one read group set per file per sample. For BAM files,
// read
// groups are considered to share a sample if they have identical
// sample
// names. Furthermore, all reads for each file which do not belong to a
// read
// group, if any, will be grouped into a single read group set per-file.
// "MERGE_ALL" - Includes all read groups in all imported files into a
// single read group
// set. Requires that the headers for all imported files are equivalent.
// All
// reads which do not belong to a read group, if any, will be grouped
// into a
// separate read group set.
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](https://samtools.github.io/hts-specs/SAMv1.pdf)
// in Google Cloud Storage.
// Those URIs can include wildcards (*), but do not add or
// remove
// matching files before import has completed.
//
// Note that Google Cloud Storage object listing is only
// eventually
// consistent: files added may be not be immediately visible
// to
// everyone. Thus, if using a wildcard it is preferable not to start
// the import immediately after the files are created.
SourceUris []string `json:"sourceUris,omitempty"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ImportReadGroupSetsRequest) MarshalJSON ¶
func (s *ImportReadGroupSetsRequest) MarshalJSON() ([]byte, error)
type ImportReadGroupSetsResponse ¶
ImportReadGroupSetsResponse: The read group set import response.
type ImportReadGroupSetsResponse struct {
// ReadGroupSetIds: IDs of the read group sets that were created.
ReadGroupSetIds []string `json:"readGroupSetIds,omitempty"`
// ForceSendFields is a list of field names (e.g. "ReadGroupSetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ReadGroupSetIds") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*ImportReadGroupSetsResponse) MarshalJSON ¶
func (s *ImportReadGroupSetsResponse) MarshalJSON() ([]byte, error)
type ImportVariantsRequest ¶
ImportVariantsRequest: The variant data import request.
type ImportVariantsRequest struct {
// Format: The format of the variant data being imported. If
// unspecified, defaults to
// to `VCF`.
//
// Possible values:
// "FORMAT_UNSPECIFIED"
// "FORMAT_VCF" - VCF (Variant Call Format). The VCF files may be gzip
// compressed. gVCF is
// also supported. Disclaimer: gzip VCF imports are currently much
// slower
// than equivalent uncompressed VCF imports. For this reason,
// uncompressed
// VCF is currently recommended for imports with more than 1GB
// combined
// uncompressed size, or for time sensitive imports.
// "FORMAT_COMPLETE_GENOMICS" - Complete Genomics masterVarBeta
// format. The masterVarBeta files may
// be bzip2 compressed.
Format string `json:"format,omitempty"`
// InfoMergeConfig: A mapping between info field keys and the
// InfoMergeOperations to
// be performed on them. This is plumbed down to the
// MergeVariantRequests
// generated by the resulting import job.
InfoMergeConfig map[string]string `json:"infoMergeConfig,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/
// WildcardNames).
// 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"`
// ForceSendFields is a list of field names (e.g. "Format") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Format") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ImportVariantsRequest) MarshalJSON ¶
func (s *ImportVariantsRequest) MarshalJSON() ([]byte, error)
type ImportVariantsResponse ¶
ImportVariantsResponse: The variant data import response.
type ImportVariantsResponse struct {
// CallSetIds: IDs of the call sets created during the import.
CallSetIds []string `json:"callSetIds,omitempty"`
// ForceSendFields is a list of field names (e.g. "CallSetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CallSetIds") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ImportVariantsResponse) MarshalJSON ¶
func (s *ImportVariantsResponse) MarshalJSON() ([]byte, error)
type LinearAlignment ¶
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 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.
//
// Specifically, this is -10 log10 Pr(mapping position is wrong),
// rounded to
// the nearest integer.
MappingQuality int64 `json:"mappingQuality,omitempty"`
// Position: The position of this alignment.
Position *Position `json:"position,omitempty"`
// ForceSendFields is a list of field names (e.g. "Cigar") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Cigar") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*LinearAlignment) MarshalJSON ¶
func (s *LinearAlignment) MarshalJSON() ([]byte, error)
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ListBasesResponse) MarshalJSON ¶
func (s *ListBasesResponse) MarshalJSON() ([]byte, error)
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "BucketWidth") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "BucketWidth") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ListCoverageBucketsResponse) MarshalJSON ¶
func (s *ListCoverageBucketsResponse) MarshalJSON() ([]byte, error)
type ListDatasetsResponse ¶
ListDatasetsResponse: The dataset list response.
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Datasets") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Datasets") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ListDatasetsResponse) MarshalJSON ¶
func (s *ListDatasetsResponse) MarshalJSON() ([]byte, error)
type ListOperationsResponse ¶
ListOperationsResponse: The response message for Operations.ListOperations.
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ListOperationsResponse) MarshalJSON ¶
func (s *ListOperationsResponse) MarshalJSON() ([]byte, error)
type MergeVariantsRequest ¶
type MergeVariantsRequest struct {
// InfoMergeConfig: A mapping between info field keys and the
// InfoMergeOperations to
// be performed on them.
InfoMergeConfig map[string]string `json:"infoMergeConfig,omitempty"`
// VariantSetId: The destination variant set.
VariantSetId string `json:"variantSetId,omitempty"`
// Variants: The variants to be merged with existing variants.
Variants []*Variant `json:"variants,omitempty"`
// ForceSendFields is a list of field names (e.g. "InfoMergeConfig") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "InfoMergeConfig") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*MergeVariantsRequest) MarshalJSON ¶
func (s *MergeVariantsRequest) MarshalJSON() ([]byte, error)
type Operation ¶
Operation: This resource represents a long-running operation that is the result of a network API call.
type Operation struct {
// Done: If the value is `false`, it means the operation is still in
// progress.
// If true, the operation is completed, and either `error` or `response`
// is
// available.
Done bool `json:"done,omitempty"`
// Error: The error result of the operation in case of failure or
// cancellation.
Error *Status `json:"error,omitempty"`
// Metadata: An OperationMetadata object. This will always be returned
// with the Operation.
Metadata googleapi.RawMessage `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, an ImportReadGroupSetsResponse
// is returned. If importing Variants, an ImportVariantsResponse is
// returned. For pipelines and exports, an empty response is returned.
Response googleapi.RawMessage `json:"response,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Done") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Done") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Operation) MarshalJSON ¶
func (s *Operation) MarshalJSON() ([]byte, error)
type OperationEvent ¶
OperationEvent: An event that occurred during an Operation.
type OperationEvent struct {
// Description: Required description of event.
Description string `json:"description,omitempty"`
// EndTime: Optional time of when event finished. An event can have a
// start time and no
// finish time. If an event has a finish time, there must be a start
// time.
EndTime string `json:"endTime,omitempty"`
// StartTime: Optional time of when event started.
StartTime string `json:"startTime,omitempty"`
// ForceSendFields is a list of field names (e.g. "Description") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Description") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*OperationEvent) MarshalJSON ¶
func (s *OperationEvent) MarshalJSON() ([]byte, error)
type OperationMetadata ¶
OperationMetadata: Metadata describing an Operation.
type OperationMetadata struct {
// ClientId: This field is deprecated. Use `labels` instead. Optionally
// provided by the
// caller when submitting the request that creates the operation.
ClientId string `json:"clientId,omitempty"`
// CreateTime: The time at which the job was submitted to the Genomics
// service.
CreateTime string `json:"createTime,omitempty"`
// EndTime: The time at which the job stopped running.
EndTime string `json:"endTime,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"`
// Labels: Optionally provided by the caller when submitting the request
// that creates
// the operation.
Labels map[string]string `json:"labels,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 googleapi.RawMessage `json:"request,omitempty"`
// RuntimeMetadata: Runtime metadata on this Operation.
RuntimeMetadata googleapi.RawMessage `json:"runtimeMetadata,omitempty"`
// StartTime: The time at which the job began to run.
StartTime string `json:"startTime,omitempty"`
// ForceSendFields is a list of field names (e.g. "ClientId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ClientId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*OperationMetadata) MarshalJSON ¶
func (s *OperationMetadata) MarshalJSON() ([]byte, error)
type OperationsCancelCall ¶
type OperationsCancelCall struct {
// contains filtered or unexported fields
}
func (*OperationsCancelCall) Context ¶
func (c *OperationsCancelCall) Context(ctx context.Context) *OperationsCancelCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*OperationsCancelCall) Do ¶
func (c *OperationsCancelCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.operations.cancel" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*OperationsCancelCall) Header ¶
func (c *OperationsCancelCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type OperationsGetCall ¶
type OperationsGetCall struct {
// contains filtered or unexported fields
}
func (*OperationsGetCall) Context ¶
func (c *OperationsGetCall) Context(ctx context.Context) *OperationsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*OperationsGetCall) Do ¶
func (c *OperationsGetCall) Do(opts ...googleapi.CallOption) (*Operation, error)
Do executes the "genomics.operations.get" call. Exactly one of *Operation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Operation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*OperationsGetCall) Header ¶
func (c *OperationsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*OperationsGetCall) IfNoneMatch ¶
func (c *OperationsGetCall) IfNoneMatch(entityTag string) *OperationsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type OperationsListCall ¶
type OperationsListCall struct {
// contains filtered or unexported fields
}
func (*OperationsListCall) Context ¶
func (c *OperationsListCall) Context(ctx context.Context) *OperationsListCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*OperationsListCall) Do ¶
func (c *OperationsListCall) Do(opts ...googleapi.CallOption) (*ListOperationsResponse, error)
Do executes the "genomics.operations.list" call. Exactly one of *ListOperationsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *ListOperationsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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. The following filter fields are supported:
* projectId: Required. Corresponds to
OperationMetadata.projectId.
* createTime: The time this job was created, in seconds from the
[epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=`
and/or `<=`
operators.
* status: Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
one status may be specified.
* labels.key where key is a label key.
Examples:
* `projectId = my-project AND createTime >= 1432140000` * `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING` * `projectId = my-project AND labels.color = *` * `projectId = my-project AND labels.color = red`
func (*OperationsListCall) Header ¶
func (c *OperationsListCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*OperationsListCall) IfNoneMatch ¶
func (c *OperationsListCall) IfNoneMatch(entityTag string) *OperationsListCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
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.
func (*OperationsListCall) Pages ¶
func (c *OperationsListCall) Pages(ctx context.Context, f func(*ListOperationsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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 or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation.
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 Policy ¶
Policy: Defines an Identity and Access Management (IAM) policy. It is used to specify access control policies for Cloud Platform resources.
A `Policy` consists of a list of `bindings`. A `Binding` binds a list of `members` to a `role`, where the members can be user accounts, Google groups, Google domains, and service accounts. A `role` is a named list of permissions defined by IAM.
**Example**
{
"bindings": [
{
"role": "roles/owner",
"members": [
"user:mike@example.com",
"group:admins@example.com",
"domain:google.com",
"serviceAccount:my-other-app@appspot.gserviceaccount.com",
]
},
{
"role": "roles/viewer",
"members": ["user:sean@example.com"]
}
]
}
For a description of IAM and its features, see the [IAM developer's guide](https://cloud.google.com/iam).
type Policy struct {
// Bindings: Associates a list of `members` to a `role`.
// `bindings` with no members will result in an error.
Bindings []*Binding `json:"bindings,omitempty"`
// Etag: `etag` is used for optimistic concurrency control as a way to
// help
// prevent simultaneous updates of a policy from overwriting each
// other.
// It is strongly suggested that systems make use of the `etag` in
// the
// read-modify-write cycle to perform policy updates in order to avoid
// race
// conditions: An `etag` is returned in the response to `getIamPolicy`,
// and
// systems are expected to put that etag in the request to
// `setIamPolicy` to
// ensure that their change will be applied to the same version of the
// policy.
//
// If no `etag` is provided in the call to `setIamPolicy`, then the
// existing
// policy is overwritten blindly.
Etag string `json:"etag,omitempty"`
// Version: Version of the `Policy`. The default version is 0.
Version int64 `json:"version,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Bindings") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Bindings") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Policy) MarshalJSON ¶
func (s *Policy) MarshalJSON() ([]byte, error)
type Position ¶
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 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"`
// ForceSendFields is a list of field names (e.g. "Position") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Position") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Position) MarshalJSON ¶
func (s *Position) MarshalJSON() ([]byte, error)
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 display name of the program. This is typically the
// colloquial name of
// the tool used, for example 'bwa' or 'picard'.
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"`
// ForceSendFields is a list of field names (e.g. "CommandLine") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CommandLine") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Program) MarshalJSON ¶
func (s *Program) MarshalJSON() ([]byte, error)
type Range ¶
Range: A 0-based half-open genomic coordinate range for search requests.
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"`
// ForceSendFields is a list of field names (e.g. "End") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "End") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Range) MarshalJSON ¶
func (s *Range) MarshalJSON() ([]byte, error)
type Read ¶
Read: A read alignment describes a linear alignment of a string of DNA to a reference sequence, 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.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
### Reverse-stranded reads
Mapped reads (reads having a non-null `alignment`) can be aligned to either the forward or the reverse strand of their associated reference. Strandedness of a mapped read is encoded by `alignment.position.reverseStrand`.
If we consider the reference to be a forward-stranded coordinate space of `[0, reference.length)` with `0` as the left-most position and `reference.length` as the right-most position, reads are always aligned left to right. That is, `alignment.position.position` always refers to the left-most reference coordinate and `alignment.cigar` describes the alignment of this read to the reference from left to right. All per-base fields such as `alignedSequence` and `alignedQuality` share this same left-to-right orientation; this is true of reads which are aligned to either strand. For reverse-stranded reads, this means that `alignedSequence` is the reverse complement of the bases that were originally reported by the sequencing machine.
### 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 Read struct {
// AlignedQuality: The quality of the read sequence contained in this
// alignment record
// (equivalent to QUAL in SAM).
// `alignedSequence` and `alignedQuality` may be shorter than the full
// read
// sequence and quality. This will occur if the alignment is part of
// a
// chimeric alignment, or if the read was trimmed. When this occurs, the
// CIGAR
// for this read will begin/end with a hard clip operator that will
// indicate
// the length of the excised sequence.
AlignedQuality []int64 `json:"alignedQuality,omitempty"`
// AlignedSequence: The bases of the read sequence contained in this
// alignment record,
// **without CIGAR operations applied** (equivalent to SEQ in
// SAM).
// `alignedSequence` and `alignedQuality` may be
// shorter than the full read sequence and quality. This will occur if
// the
// alignment is part of a chimeric alignment, or if the read was
// trimmed. When
// this occurs, the CIGAR for this read will begin/end with a hard
// clip
// operator that will indicate the length of the excised sequence.
AlignedSequence string `json:"alignedSequence,omitempty"`
// Alignment: The linear alignment for this alignment record. This field
// is null for
// unmapped reads.
Alignment *LinearAlignment `json:"alignment,omitempty"`
// DuplicateFragment: The fragment is a PCR or optical duplicate (SAM
// flag 0x400).
DuplicateFragment bool `json:"duplicateFragment,omitempty"`
// FailedVendorQualityChecks: Whether this read did not pass filters,
// such as platform or vendor quality
// controls (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, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `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. A read
// belongs to exactly
// one read group. This is a server-generated ID which is distinct from
// SAM's
// RG tag (for that value, see
// ReadGroup.name).
ReadGroupId string `json:"readGroupId,omitempty"`
// ReadGroupSetId: The ID of the read group set this read belongs to. A
// read belongs 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"`
// ForceSendFields is a list of field names (e.g. "AlignedQuality") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AlignedQuality") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*Read) MarshalJSON ¶
func (s *Read) MarshalJSON() ([]byte, error)
type ReadGroup ¶
ReadGroup: A read group is all the data that's processed the same way by the sequencer.
type ReadGroup struct {
// DatasetId: The dataset to which this read group belongs.
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 name.
Id string `json:"id,omitempty"`
// Info: A map of additional read group information. This must be of the
// form
// map<string, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `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.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// SampleId: A client-supplied sample identifier for the reads in this
// read group.
SampleId string `json:"sampleId,omitempty"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ReadGroup) MarshalJSON ¶
func (s *ReadGroup) MarshalJSON() ([]byte, error)
type ReadGroupSet ¶
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.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
type ReadGroupSet struct {
// DatasetId: The dataset to which this read group set belongs.
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 map[string][]interface{} `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 to which the reads in this read
// group set are aligned.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ReadGroupSet) MarshalJSON ¶
func (s *ReadGroupSet) MarshalJSON() ([]byte, error)
type ReadgroupsetsCoveragebucketsListCall ¶
type ReadgroupsetsCoveragebucketsListCall struct {
// contains filtered or unexported fields
}
func (*ReadgroupsetsCoveragebucketsListCall) Context ¶
func (c *ReadgroupsetsCoveragebucketsListCall) Context(ctx context.Context) *ReadgroupsetsCoveragebucketsListCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadgroupsetsCoveragebucketsListCall) Do ¶
func (c *ReadgroupsetsCoveragebucketsListCall) Do(opts ...googleapi.CallOption) (*ListCoverageBucketsResponse, error)
Do executes the "genomics.readgroupsets.coveragebuckets.list" call. Exactly one of *ListCoverageBucketsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *ListCoverageBucketsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *ReadgroupsetsCoveragebucketsListCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReadgroupsetsCoveragebucketsListCall) IfNoneMatch ¶
func (c *ReadgroupsetsCoveragebucketsListCall) IfNoneMatch(entityTag string) *ReadgroupsetsCoveragebucketsListCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
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) Pages ¶
func (c *ReadgroupsetsCoveragebucketsListCall) Pages(ctx context.Context, f func(*ListCoverageBucketsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.
type ReadgroupsetsDeleteCall ¶
type ReadgroupsetsDeleteCall struct {
// contains filtered or unexported fields
}
func (*ReadgroupsetsDeleteCall) Context ¶
func (c *ReadgroupsetsDeleteCall) Context(ctx context.Context) *ReadgroupsetsDeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadgroupsetsDeleteCall) Do ¶
func (c *ReadgroupsetsDeleteCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.readgroupsets.delete" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReadgroupsetsDeleteCall) Header ¶
func (c *ReadgroupsetsDeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type ReadgroupsetsExportCall ¶
type ReadgroupsetsExportCall struct {
// contains filtered or unexported fields
}
func (*ReadgroupsetsExportCall) Context ¶
func (c *ReadgroupsetsExportCall) Context(ctx context.Context) *ReadgroupsetsExportCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadgroupsetsExportCall) Do ¶
func (c *ReadgroupsetsExportCall) Do(opts ...googleapi.CallOption) (*Operation, error)
Do executes the "genomics.readgroupsets.export" call. Exactly one of *Operation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Operation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReadgroupsetsExportCall) Header ¶
func (c *ReadgroupsetsExportCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type ReadgroupsetsGetCall ¶
type ReadgroupsetsGetCall struct {
// contains filtered or unexported fields
}
func (*ReadgroupsetsGetCall) Context ¶
func (c *ReadgroupsetsGetCall) Context(ctx context.Context) *ReadgroupsetsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadgroupsetsGetCall) Do ¶
func (c *ReadgroupsetsGetCall) Do(opts ...googleapi.CallOption) (*ReadGroupSet, error)
Do executes the "genomics.readgroupsets.get" call. Exactly one of *ReadGroupSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *ReadGroupSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReadgroupsetsGetCall) Header ¶
func (c *ReadgroupsetsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReadgroupsetsGetCall) IfNoneMatch ¶
func (c *ReadgroupsetsGetCall) IfNoneMatch(entityTag string) *ReadgroupsetsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type ReadgroupsetsImportCall ¶
type ReadgroupsetsImportCall struct {
// contains filtered or unexported fields
}
func (*ReadgroupsetsImportCall) Context ¶
func (c *ReadgroupsetsImportCall) Context(ctx context.Context) *ReadgroupsetsImportCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadgroupsetsImportCall) Do ¶
func (c *ReadgroupsetsImportCall) Do(opts ...googleapi.CallOption) (*Operation, error)
Do executes the "genomics.readgroupsets.import" call. Exactly one of *Operation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Operation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReadgroupsetsImportCall) Header ¶
func (c *ReadgroupsetsImportCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type ReadgroupsetsPatchCall ¶
type ReadgroupsetsPatchCall struct {
// contains filtered or unexported fields
}
func (*ReadgroupsetsPatchCall) Context ¶
func (c *ReadgroupsetsPatchCall) Context(ctx context.Context) *ReadgroupsetsPatchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadgroupsetsPatchCall) Do ¶
func (c *ReadgroupsetsPatchCall) Do(opts ...googleapi.CallOption) (*ReadGroupSet, error)
Do executes the "genomics.readgroupsets.patch" call. Exactly one of *ReadGroupSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *ReadGroupSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *ReadgroupsetsPatchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReadgroupsetsPatchCall) UpdateMask ¶
func (c *ReadgroupsetsPatchCall) UpdateMask(updateMask string) *ReadgroupsetsPatchCall
UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. Supported fields:
* name. * referenceSetId.
Leaving `updateMask` unset is equivalent to specifying all mutable fields.
type ReadgroupsetsSearchCall ¶
type ReadgroupsetsSearchCall struct {
// contains filtered or unexported fields
}
func (*ReadgroupsetsSearchCall) Context ¶
func (c *ReadgroupsetsSearchCall) Context(ctx context.Context) *ReadgroupsetsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadgroupsetsSearchCall) Do ¶
func (c *ReadgroupsetsSearchCall) Do(opts ...googleapi.CallOption) (*SearchReadGroupSetsResponse, error)
Do executes the "genomics.readgroupsets.search" call. Exactly one of *SearchReadGroupSetsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchReadGroupSetsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReadgroupsetsSearchCall) Header ¶
func (c *ReadgroupsetsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReadgroupsetsSearchCall) Pages ¶
func (c *ReadgroupsetsSearchCall) Pages(ctx context.Context, f func(*SearchReadGroupSetsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. See ImportReadGroupSets for caveats.
func (*ReadgroupsetsService) Get ¶
func (r *ReadgroupsetsService) Get(readGroupSetId string) *ReadgroupsetsGetCall
Get: Gets a read group set by ID.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*ReadgroupsetsService) Import ¶
func (r *ReadgroupsetsService) Import(importreadgroupsetsrequest *ImportReadGroupSetsRequest) *ReadgroupsetsImportCall
Import: Creates read group sets by asynchronously importing the provided information.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
The caller must have WRITE permissions to the dataset.
## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
- Tags will be converted to strings - tag types are not preserved - Comments (`@CO`) in the input file header will not be preserved - Original header order of references (`@SQ`) will not be preserved - Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed - Unmapped reads will be stripped of positional information (reference name and position)
func (*ReadgroupsetsService) Patch ¶
func (r *ReadgroupsetsService) Patch(readGroupSetId string, readgroupset *ReadGroupSet) *ReadgroupsetsPatchCall
Patch: Updates a read group set.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
This method supports patch semantics.
func (*ReadgroupsetsService) Search ¶
func (r *ReadgroupsetsService) Search(searchreadgroupsetsrequest *SearchReadGroupSetsRequest) *ReadgroupsetsSearchCall
Search: Searches for read group sets matching the criteria.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.searchReadGroupSets](http s://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readm ethods.avdl#L135).
type ReadsSearchCall ¶
type ReadsSearchCall struct {
// contains filtered or unexported fields
}
func (*ReadsSearchCall) Context ¶
func (c *ReadsSearchCall) Context(ctx context.Context) *ReadsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReadsSearchCall) Do ¶
func (c *ReadsSearchCall) Do(opts ...googleapi.CallOption) (*SearchReadsResponse, error)
Do executes the "genomics.reads.search" call. Exactly one of *SearchReadsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchReadsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReadsSearchCall) Header ¶
func (c *ReadsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReadsSearchCall) Pages ¶
func (c *ReadsSearchCall) Pages(ctx context.Context, f func(*SearchReadsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested read group sets are aligned.
If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads.
All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (by reference sequence, then position). Reads with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield reads in the same order across their respective streams of paginated responses.
Implements [GlobalAllianceApi.searchReads](https://github. com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl #L85).
type Reference ¶
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.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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. For
// example, 9606 for human.
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. Typically
// specifies a FASTA
// format file.
SourceUri string `json:"sourceUri,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Id") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Id") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Reference) MarshalJSON ¶
func (s *Reference) MarshalJSON() ([]byte, error)
type ReferenceBound ¶
ReferenceBound: ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
type ReferenceBound struct {
// ReferenceName: The name of the reference associated with this
// reference bound.
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"`
// ForceSendFields is a list of field names (e.g. "ReferenceName") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ReferenceName") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ReferenceBound) MarshalJSON ¶
func (s *ReferenceBound) MarshalJSON() ([]byte, error)
type ReferenceSet ¶
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.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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 (for
// example, 9606 for human)
// indicating the species which this reference set is intended to model.
// Note
// that contained references may specify a different `ncbiTaxonId`,
// as
// assemblies may contain reference sequences which do not belong to
// the
// modeled species, for example EBV in a human reference genome.
NcbiTaxonId 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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "AssemblyId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AssemblyId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*ReferenceSet) MarshalJSON ¶
func (s *ReferenceSet) MarshalJSON() ([]byte, error)
type ReferencesBasesListCall ¶
type ReferencesBasesListCall struct {
// contains filtered or unexported fields
}
func (*ReferencesBasesListCall) Context ¶
func (c *ReferencesBasesListCall) Context(ctx context.Context) *ReferencesBasesListCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReferencesBasesListCall) Do ¶
func (c *ReferencesBasesListCall) Do(opts ...googleapi.CallOption) (*ListBasesResponse, error)
Do executes the "genomics.references.bases.list" call. Exactly one of *ListBasesResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *ListBasesResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *ReferencesBasesListCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReferencesBasesListCall) IfNoneMatch ¶
func (c *ReferencesBasesListCall) IfNoneMatch(entityTag string) *ReferencesBasesListCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
func (*ReferencesBasesListCall) PageSize ¶
func (c *ReferencesBasesListCall) PageSize(pageSize int64) *ReferencesBasesListCall
PageSize sets the optional parameter "pageSize": The maximum number of bases to return in a single page. If unspecified, defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base pairs).
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) Pages ¶
func (c *ReferencesBasesListCall) Pages(ctx context.Context, f func(*ListBasesResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.getReferenceBases](https: //github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referen cemethods.avdl#L221).
type ReferencesGetCall ¶
type ReferencesGetCall struct {
// contains filtered or unexported fields
}
func (*ReferencesGetCall) Context ¶
func (c *ReferencesGetCall) Context(ctx context.Context) *ReferencesGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReferencesGetCall) Do ¶
func (c *ReferencesGetCall) Do(opts ...googleapi.CallOption) (*Reference, error)
Do executes the "genomics.references.get" call. Exactly one of *Reference or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Reference.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReferencesGetCall) Header ¶
func (c *ReferencesGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReferencesGetCall) IfNoneMatch ¶
func (c *ReferencesGetCall) IfNoneMatch(entityTag string) *ReferencesGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type ReferencesSearchCall ¶
type ReferencesSearchCall struct {
// contains filtered or unexported fields
}
func (*ReferencesSearchCall) Context ¶
func (c *ReferencesSearchCall) Context(ctx context.Context) *ReferencesSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReferencesSearchCall) Do ¶
func (c *ReferencesSearchCall) Do(opts ...googleapi.CallOption) (*SearchReferencesResponse, error)
Do executes the "genomics.references.search" call. Exactly one of *SearchReferencesResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchReferencesResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReferencesSearchCall) Header ¶
func (c *ReferencesSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReferencesSearchCall) Pages ¶
func (c *ReferencesSearchCall) Pages(ctx context.Context, f func(*SearchReferencesResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.getReference](https://git hub.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemet hods.avdl#L158).
func (*ReferencesService) Search ¶
func (r *ReferencesService) Search(searchreferencesrequest *SearchReferencesRequest) *ReferencesSearchCall
Search: Searches for references which match the given criteria.
For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.searchReferences](https:/ /github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referenc emethods.avdl#L146).
type ReferencesetsGetCall ¶
type ReferencesetsGetCall struct {
// contains filtered or unexported fields
}
func (*ReferencesetsGetCall) Context ¶
func (c *ReferencesetsGetCall) Context(ctx context.Context) *ReferencesetsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReferencesetsGetCall) Do ¶
func (c *ReferencesetsGetCall) Do(opts ...googleapi.CallOption) (*ReferenceSet, error)
Do executes the "genomics.referencesets.get" call. Exactly one of *ReferenceSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *ReferenceSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReferencesetsGetCall) Header ¶
func (c *ReferencesetsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReferencesetsGetCall) IfNoneMatch ¶
func (c *ReferencesetsGetCall) IfNoneMatch(entityTag string) *ReferencesetsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type ReferencesetsSearchCall ¶
type ReferencesetsSearchCall struct {
// contains filtered or unexported fields
}
func (*ReferencesetsSearchCall) Context ¶
func (c *ReferencesetsSearchCall) Context(ctx context.Context) *ReferencesetsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*ReferencesetsSearchCall) Do ¶
func (c *ReferencesetsSearchCall) Do(opts ...googleapi.CallOption) (*SearchReferenceSetsResponse, error)
Do executes the "genomics.referencesets.search" call. Exactly one of *SearchReferenceSetsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchReferenceSetsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*ReferencesetsSearchCall) Header ¶
func (c *ReferencesetsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*ReferencesetsSearchCall) Pages ¶
func (c *ReferencesetsSearchCall) Pages(ctx context.Context, f func(*SearchReferenceSetsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.getReferenceSet](https:// github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reference methods.avdl#L83).
func (*ReferencesetsService) Search ¶
func (r *ReferencesetsService) Search(searchreferencesetsrequest *SearchReferenceSetsRequest) *ReferencesetsSearchCall
Search: Searches for reference sets which match the given criteria.
For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.searchReferenceSets](http s://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/refer encemethods.avdl#L71)
type RuntimeMetadata ¶
RuntimeMetadata: Runtime metadata that will be populated in the runtimeMetadata field of the Operation associated with a RunPipeline execution.
type RuntimeMetadata struct {
// ComputeEngine: Execution information specific to Google Compute
// Engine.
ComputeEngine *ComputeEngine `json:"computeEngine,omitempty"`
// ForceSendFields is a list of field names (e.g. "ComputeEngine") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "ComputeEngine") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*RuntimeMetadata) MarshalJSON ¶
func (s *RuntimeMetadata) MarshalJSON() ([]byte, error)
type SearchAnnotationSetsRequest ¶
type SearchAnnotationSetsRequest struct {
// DatasetIds: Required. The dataset IDs to search within. Caller must
// have `READ` access
// to these datasets.
DatasetIds []string `json:"datasetIds,omitempty"`
// Name: Only return annotations sets for which a substring of the name
// matches this
// string (case insensitive).
Name string `json:"name,omitempty"`
// PageSize: The maximum number of results to return in a single page.
// If unspecified,
// defaults to 128. 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"`
// ReferenceSetId: If specified, only annotation sets associated with
// the given reference set
// are returned.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// Types: If specified, only annotation sets that have any of these
// types are
// returned.
//
// Possible values:
// "ANNOTATION_TYPE_UNSPECIFIED"
// "GENERIC" - A `GENERIC` annotation type should be used when no
// other annotation
// type will suffice. This represents an untyped annotation of the
// reference
// genome.
// "VARIANT" - A `VARIANT` annotation type.
// "GENE" - A `GENE` annotation type represents the existence of a
// gene at the
// associated reference coordinates. The start coordinate is typically
// the
// gene's transcription start site and the end is typically the end of
// the
// gene's last exon.
// "TRANSCRIPT" - A `TRANSCRIPT` annotation type represents the
// assertion that a
// particular region of the reference genome may be transcribed as RNA.
Types []string `json:"types,omitempty"`
// ForceSendFields is a list of field names (e.g. "DatasetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetIds") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchAnnotationSetsRequest) MarshalJSON ¶
func (s *SearchAnnotationSetsRequest) MarshalJSON() ([]byte, error)
type SearchAnnotationSetsResponse ¶
type SearchAnnotationSetsResponse struct {
// AnnotationSets: The matching annotation sets.
AnnotationSets []*AnnotationSet `json:"annotationSets,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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "AnnotationSets") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AnnotationSets") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*SearchAnnotationSetsResponse) MarshalJSON ¶
func (s *SearchAnnotationSetsResponse) MarshalJSON() ([]byte, error)
type SearchAnnotationsRequest ¶
type SearchAnnotationsRequest struct {
// AnnotationSetIds: Required. The annotation sets to search within. The
// caller must have
// `READ` access to these annotation sets.
// All queried annotation sets must have the same type.
AnnotationSetIds []string `json:"annotationSetIds,omitempty"`
// End: The end position of the range on the reference, 0-based
// exclusive. If
// referenceId or
// referenceName
// must be specified, Defaults to the length of the reference.
End int64 `json:"end,omitempty,string"`
// PageSize: The maximum number of results to return in a single page.
// If unspecified,
// defaults 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"`
// ReferenceId: The ID of the reference to query.
ReferenceId string `json:"referenceId,omitempty"`
// ReferenceName: The name of the reference to query, within the
// reference set associated
// with this query.
ReferenceName string `json:"referenceName,omitempty"`
// Start: The start position of the range on the reference, 0-based
// inclusive. If
// specified,
// referenceId or
// referenceName
// must be specified. Defaults to 0.
Start int64 `json:"start,omitempty,string"`
// ForceSendFields is a list of field names (e.g. "AnnotationSetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AnnotationSetIds") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*SearchAnnotationsRequest) MarshalJSON ¶
func (s *SearchAnnotationsRequest) MarshalJSON() ([]byte, error)
type SearchAnnotationsResponse ¶
type SearchAnnotationsResponse struct {
// Annotations: The matching annotations.
Annotations []*Annotation `json:"annotations,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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Annotations") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Annotations") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchAnnotationsResponse) MarshalJSON ¶
func (s *SearchAnnotationsResponse) MarshalJSON() ([]byte, error)
type SearchCallSetsRequest ¶
SearchCallSetsRequest: The call set search request.
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 results to return in a single page.
// If unspecified,
// defaults to 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"`
// VariantSetIds: Restrict the query to call sets within the given
// variant sets. At least one
// ID must be provided.
VariantSetIds []string `json:"variantSetIds,omitempty"`
// ForceSendFields is a list of field names (e.g. "Name") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Name") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchCallSetsRequest) MarshalJSON ¶
func (s *SearchCallSetsRequest) MarshalJSON() ([]byte, error)
type SearchCallSetsResponse ¶
SearchCallSetsResponse: The call set search response.
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "CallSets") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CallSets") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchCallSetsResponse) MarshalJSON ¶
func (s *SearchCallSetsResponse) MarshalJSON() ([]byte, error)
type SearchReadGroupSetsRequest ¶
SearchReadGroupSetsRequest: The read group set search request.
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: The maximum number of results to return in a single page.
// If unspecified,
// defaults 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"`
// ForceSendFields is a list of field names (e.g. "DatasetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetIds") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReadGroupSetsRequest) MarshalJSON ¶
func (s *SearchReadGroupSetsRequest) MarshalJSON() ([]byte, error)
type SearchReadGroupSetsResponse ¶
SearchReadGroupSetsResponse: The read group set search response.
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReadGroupSetsResponse) MarshalJSON ¶
func (s *SearchReadGroupSetsResponse) MarshalJSON() ([]byte, error)
type SearchReadsRequest ¶
SearchReadsRequest: The read search request.
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: The maximum number of results to return in a single page.
// If unspecified,
// defaults 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. If unspecified, all reads
// (mapped
// and unmapped) 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"`
// ForceSendFields is a list of field names (e.g. "End") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "End") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReadsRequest) MarshalJSON ¶
func (s *SearchReadsRequest) MarshalJSON() ([]byte, error)
type SearchReadsResponse ¶
SearchReadsResponse: The read search response.
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 contiguously and are 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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Alignments") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Alignments") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReadsResponse) MarshalJSON ¶
func (s *SearchReadsResponse) MarshalJSON() ([]byte, error)
type SearchReferenceSetsRequest ¶
type SearchReferenceSetsRequest struct {
// Accessions: If present, return reference sets for which a prefix of
// any of
// sourceAccessions
// match any of these strings. Accession numbers typically have a main
// number
// and a version, for example `NC_000001.11`.
Accessions []string `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 reference sets for which
// the
// md5checksum matches exactly.
Md5checksums []string `json:"md5checksums,omitempty"`
// PageSize: The maximum number of results to return in a single page.
// If unspecified,
// defaults to 1024. The maximum value is 4096.
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"`
// ForceSendFields is a list of field names (e.g. "Accessions") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Accessions") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReferenceSetsRequest) MarshalJSON ¶
func (s *SearchReferenceSetsRequest) MarshalJSON() ([]byte, error)
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReferenceSetsResponse) MarshalJSON ¶
func (s *SearchReferenceSetsResponse) MarshalJSON() ([]byte, error)
type SearchReferencesRequest ¶
type SearchReferencesRequest struct {
// Accessions: If present, return references for which a prefix of any
// of
// sourceAccessions match
// any of these strings. Accession numbers typically have a main number
// and a
// version, for example `GCF_000001405.26`.
Accessions []string `json:"accessions,omitempty"`
// Md5checksums: If present, return references for which the
// md5checksum matches exactly.
Md5checksums []string `json:"md5checksums,omitempty"`
// PageSize: The maximum number of results to return in a single page.
// If unspecified,
// defaults to 1024. The maximum value is 4096.
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"`
// ForceSendFields is a list of field names (e.g. "Accessions") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Accessions") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReferencesRequest) MarshalJSON ¶
func (s *SearchReferencesRequest) MarshalJSON() ([]byte, error)
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchReferencesResponse) MarshalJSON ¶
func (s *SearchReferencesResponse) MarshalJSON() ([]byte, error)
type SearchVariantSetsRequest ¶
SearchVariantSetsRequest: The search variant sets request.
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 results to return in a single page.
// If unspecified,
// defaults to 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"`
// ForceSendFields is a list of field names (e.g. "DatasetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetIds") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchVariantSetsRequest) MarshalJSON ¶
func (s *SearchVariantSetsRequest) MarshalJSON() ([]byte, error)
type SearchVariantSetsResponse ¶
SearchVariantSetsResponse: The search variant sets response.
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchVariantSetsResponse) MarshalJSON ¶
func (s *SearchVariantSetsResponse) MarshalJSON() ([]byte, error)
type SearchVariantsRequest ¶
SearchVariantsRequest: The variant search request.
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.
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 in a single page.
// Note that this
// limit may be exceeded in the event that a matching variant contains
// more
// calls than the requested maximum. If unspecified, defaults to 5000.
// The
// maximum value is 10000.
MaxCalls int64 `json:"maxCalls,omitempty"`
// PageSize: The maximum number of variants to return in a single page.
// If unspecified,
// defaults to 5000. The maximum value is 10000.
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"`
// ForceSendFields is a list of field names (e.g. "CallSetIds") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CallSetIds") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchVariantsRequest) MarshalJSON ¶
func (s *SearchVariantsRequest) MarshalJSON() ([]byte, error)
type SearchVariantsResponse ¶
SearchVariantsResponse: The variant search response.
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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "NextPageToken") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "NextPageToken") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SearchVariantsResponse) MarshalJSON ¶
func (s *SearchVariantsResponse) MarshalJSON() ([]byte, error)
type Service ¶
type Service struct {
BasePath string // API endpoint base URL
UserAgent string // optional additional User-Agent fragment
Annotations *AnnotationsService
Annotationsets *AnnotationsetsService
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 SetIamPolicyRequest ¶
SetIamPolicyRequest: Request message for `SetIamPolicy` method.
type SetIamPolicyRequest struct {
// Policy: REQUIRED: The complete policy to be applied to the
// `resource`. The size of
// the policy is limited to a few 10s of KB. An empty policy is a
// valid policy but certain Cloud Platform services (such as
// Projects)
// might reject them.
Policy *Policy `json:"policy,omitempty"`
// ForceSendFields is a list of field names (e.g. "Policy") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Policy") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*SetIamPolicyRequest) MarshalJSON ¶
func (s *SetIamPolicyRequest) MarshalJSON() ([]byte, error)
type Status ¶
Status: The `Status` type 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 three pieces of data: error code, error message, and error details. The error code should be an enum value of 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, put the localized message in the error details or localize it in 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` that 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 a 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.
- 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 Status struct {
// Code: The status code, which should be an enum value of
// 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 []googleapi.RawMessage `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 field, or localized by the client.
Message string `json:"message,omitempty"`
// ForceSendFields is a list of field names (e.g. "Code") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Code") to include in API
// requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*Status) MarshalJSON ¶
func (s *Status) MarshalJSON() ([]byte, error)
type TestIamPermissionsRequest ¶
TestIamPermissionsRequest: Request message for `TestIamPermissions` method.
type TestIamPermissionsRequest struct {
// Permissions: REQUIRED: The set of permissions to check for the
// 'resource'.
// Permissions with wildcards (such as '*' or 'storage.*') are not
// allowed.
// Allowed permissions are:
//
// * `genomics.datasets.create`
// * `genomics.datasets.delete`
// * `genomics.datasets.get`
// * `genomics.datasets.list`
// * `genomics.datasets.update`
// * `genomics.datasets.getIamPolicy`
// * `genomics.datasets.setIamPolicy`
Permissions []string `json:"permissions,omitempty"`
// ForceSendFields is a list of field names (e.g. "Permissions") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Permissions") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*TestIamPermissionsRequest) MarshalJSON ¶
func (s *TestIamPermissionsRequest) MarshalJSON() ([]byte, error)
type TestIamPermissionsResponse ¶
TestIamPermissionsResponse: Response message for `TestIamPermissions` method.
type TestIamPermissionsResponse struct {
// Permissions: A subset of `TestPermissionsRequest.permissions` that
// the caller is
// allowed.
Permissions []string `json:"permissions,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "Permissions") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Permissions") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*TestIamPermissionsResponse) MarshalJSON ¶
func (s *TestIamPermissionsResponse) MarshalJSON() ([]byte, error)
type Transcript ¶
Transcript: A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA.
type Transcript struct {
// CodingSequence: The range of the coding sequence for this transcript,
// if any. To determine
// the exact ranges of coding sequence, intersect this range with those
// of the
// exons, if any. If there are any
// exons, the
// codingSequence must start
// and end within them.
//
// Note that in some cases, the reference genome will not exactly match
// the
// observed mRNA transcript e.g. due to variance in the source genome
// from
// reference. In these cases,
// exon.frame will not necessarily
// match the expected reference reading frame and coding exon reference
// bases
// cannot necessarily be concatenated to produce the original transcript
// mRNA.
CodingSequence *CodingSequence `json:"codingSequence,omitempty"`
// Exons: The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that
// compose
// this transcript. This field should be unset for genomes where
// transcript
// splicing does not occur, for example prokaryotes.
//
// Introns are regions of the transcript that are not included in
// the
// spliced RNA product. Though not explicitly modeled here, intron
// ranges can
// be deduced; all regions of this transcript that are not exons are
// introns.
//
// Exonic sequences do not necessarily code for a translational
// product
// (amino acids). Only the regions of exons bounded by
// the
// codingSequence correspond
// to coding DNA sequence.
//
// Exons are ordered by start position and may not overlap.
Exons []*Exon `json:"exons,omitempty"`
// GeneId: The annotation ID of the gene from which this transcript is
// transcribed.
GeneId string `json:"geneId,omitempty"`
// ForceSendFields is a list of field names (e.g. "CodingSequence") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CodingSequence") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*Transcript) MarshalJSON ¶
func (s *Transcript) MarshalJSON() ([]byte, error)
type UndeleteDatasetRequest ¶
type UndeleteDatasetRequest struct {
}
type Variant ¶
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.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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 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, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `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"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "AlternateBases") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AlternateBases") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*Variant) MarshalJSON ¶
func (s *Variant) MarshalJSON() ([]byte, error)
func (*Variant) UnmarshalJSON ¶
func (s *Variant) UnmarshalJSON(data []byte) error
type VariantAnnotation ¶
type VariantAnnotation struct {
// AlternateBases: The alternate allele for this variant. If multiple
// alternate alleles
// exist at this location, create a separate variant for each one, as
// they
// may represent distinct conditions.
AlternateBases string `json:"alternateBases,omitempty"`
// ClinicalSignificance: Describes the clinical significance of a
// variant.
// It is adapted from the ClinVar controlled vocabulary for
// clinical
// significance described
// at:
// http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
//
// Possible values:
// "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
// "CLINICAL_SIGNIFICANCE_OTHER" - `OTHER` should be used when no
// other clinical significance
// value will suffice.
// "UNCERTAIN"
// "BENIGN"
// "LIKELY_BENIGN"
// "LIKELY_PATHOGENIC"
// "PATHOGENIC"
// "DRUG_RESPONSE"
// "HISTOCOMPATIBILITY"
// "CONFERS_SENSITIVITY"
// "RISK_FACTOR"
// "ASSOCIATION"
// "PROTECTIVE"
// "MULTIPLE_REPORTED" - `MULTIPLE_REPORTED` should be used when
// multiple clinical
// signficances are reported for a variant. The original
// clinical
// significance values may be provided in the `info` field.
ClinicalSignificance string `json:"clinicalSignificance,omitempty"`
// Conditions: The set of conditions associated with this variant.
// A condition describes the way a variant influences human health.
Conditions []*ClinicalCondition `json:"conditions,omitempty"`
// Effect: Effect of the variant on the coding sequence.
//
// Possible values:
// "EFFECT_UNSPECIFIED"
// "EFFECT_OTHER" - `EFFECT_OTHER` should be used when no other
// Effect
// will suffice.
// "FRAMESHIFT" - `FRAMESHIFT` indicates a mutation in which the
// insertion or
// deletion of nucleotides resulted in a frameshift change.
// "FRAME_PRESERVING_INDEL" - `FRAME_PRESERVING_INDEL` indicates a
// mutation in which a
// multiple of three nucleotides has been inserted or deleted,
// resulting
// in no change to the reading frame of the coding sequence.
// "SYNONYMOUS_SNP" - `SYNONYMOUS_SNP` indicates a single nucleotide
// polymorphism
// mutation that results in no amino acid change.
// "NONSYNONYMOUS_SNP" - `NONSYNONYMOUS_SNP` indicates a single
// nucleotide
// polymorphism mutation that results in an amino acid change.
// "STOP_GAIN" - `STOP_GAIN` indicates a mutation that leads to the
// creation
// of a stop codon at the variant site. Frameshift mutations
// creating
// downstream stop codons do not count as `STOP_GAIN`.
// "STOP_LOSS" - `STOP_LOSS` indicates a mutation that eliminates
// a
// stop codon at the variant site.
// "SPLICE_SITE_DISRUPTION" - `SPLICE_SITE_DISRUPTION` indicates that
// this variant is
// found in a splice site for the associated transcript, and alters
// the
// normal splicing pattern.
Effect string `json:"effect,omitempty"`
// GeneId: Google annotation ID of the gene affected by this variant.
// This should
// be provided when the variant is created.
GeneId string `json:"geneId,omitempty"`
// TranscriptIds: Google annotation IDs of the transcripts affected by
// this variant. These
// should be provided when the variant is created.
TranscriptIds []string `json:"transcriptIds,omitempty"`
// Type: Type has been adapted from ClinVar's list of variant types.
//
// Possible values:
// "TYPE_UNSPECIFIED"
// "TYPE_OTHER" - `TYPE_OTHER` should be used when no other Type will
// suffice.
// Further explanation of the variant type may be included in the
// info field.
// "INSERTION" - `INSERTION` indicates an insertion.
// "DELETION" - `DELETION` indicates a deletion.
// "SUBSTITUTION" - `SUBSTITUTION` indicates a block substitution
// of
// two or more nucleotides.
// "SNP" - `SNP` indicates a single nucleotide polymorphism.
// "STRUCTURAL" - `STRUCTURAL` indicates a large structural
// variant,
// including chromosomal fusions, inversions, etc.
// "CNV" - `CNV` indicates a variation in copy number.
Type string `json:"type,omitempty"`
// ForceSendFields is a list of field names (e.g. "AlternateBases") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "AlternateBases") to
// include in API requests with the JSON null value. By default, fields
// with empty values are omitted from API requests. However, any field
// with an empty value appearing in NullFields will be sent to the
// server as null. It is an error if a field in this list has a
// non-empty value. This may be used to include null fields in Patch
// requests.
NullFields []string `json:"-"`
}
func (*VariantAnnotation) MarshalJSON ¶
func (s *VariantAnnotation) MarshalJSON() ([]byte, error)
type VariantCall ¶
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 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, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `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"`
// ForceSendFields is a list of field names (e.g. "CallSetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "CallSetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*VariantCall) MarshalJSON ¶
func (s *VariantCall) MarshalJSON() ([]byte, error)
type VariantSet ¶
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.
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
type VariantSet struct {
// DatasetId: The dataset to which this variant set belongs.
DatasetId string `json:"datasetId,omitempty"`
// Description: A textual description of this variant set.
Description string `json:"description,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"`
// Name: User-specified, mutable name.
Name string `json:"name,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"`
// ReferenceSetId: The reference set to which the variant set is mapped.
// The reference set
// describes the alignment provenance of the variant set, while
// the
// `referenceBounds` describe the shape of the actual variant data.
// The
// reference set's reference names are a superset of those found in
// the
// `referenceBounds`.
//
// For example, given a variant set that is mapped to the GRCh38
// reference set
// and contains a single variant on reference 'X', `referenceBounds`
// would
// contain only an entry for 'X', while the associated reference
// set
// enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
ReferenceSetId string `json:"referenceSetId,omitempty"`
// ServerResponse contains the HTTP response code and headers from the
// server.
googleapi.ServerResponse `json:"-"`
// ForceSendFields is a list of field names (e.g. "DatasetId") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "DatasetId") to include in
// API requests with the JSON null value. By default, fields with empty
// values are omitted from API requests. However, any field with an
// empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*VariantSet) MarshalJSON ¶
func (s *VariantSet) MarshalJSON() ([]byte, error)
type VariantSetMetadata ¶
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 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, string[]> (string key mapping to a list of string
// values).
Info map[string][]interface{} `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.
//
// 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"`
// ForceSendFields is a list of field names (e.g. "Description") to
// unconditionally include in API requests. By default, fields with
// empty values are omitted from API requests. However, any non-pointer,
// non-interface field appearing in ForceSendFields will be sent to the
// server regardless of whether the field is empty or not. This may be
// used to include empty fields in Patch requests.
ForceSendFields []string `json:"-"`
// NullFields is a list of field names (e.g. "Description") to include
// in API requests with the JSON null value. By default, fields with
// empty values are omitted from API requests. However, any field with
// an empty value appearing in NullFields will be sent to the server as
// null. It is an error if a field in this list has a non-empty value.
// This may be used to include null fields in Patch requests.
NullFields []string `json:"-"`
}
func (*VariantSetMetadata) MarshalJSON ¶
func (s *VariantSetMetadata) MarshalJSON() ([]byte, error)
type VariantsCreateCall ¶
type VariantsCreateCall struct {
// contains filtered or unexported fields
}
func (*VariantsCreateCall) Context ¶
func (c *VariantsCreateCall) Context(ctx context.Context) *VariantsCreateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsCreateCall) Do ¶
func (c *VariantsCreateCall) Do(opts ...googleapi.CallOption) (*Variant, error)
Do executes the "genomics.variants.create" call. Exactly one of *Variant or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Variant.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsCreateCall) Header ¶
func (c *VariantsCreateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type VariantsDeleteCall ¶
type VariantsDeleteCall struct {
// contains filtered or unexported fields
}
func (*VariantsDeleteCall) Context ¶
func (c *VariantsDeleteCall) Context(ctx context.Context) *VariantsDeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsDeleteCall) Do ¶
func (c *VariantsDeleteCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.variants.delete" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsDeleteCall) Header ¶
func (c *VariantsDeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type VariantsGetCall ¶
type VariantsGetCall struct {
// contains filtered or unexported fields
}
func (*VariantsGetCall) Context ¶
func (c *VariantsGetCall) Context(ctx context.Context) *VariantsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsGetCall) Do ¶
func (c *VariantsGetCall) Do(opts ...googleapi.CallOption) (*Variant, error)
Do executes the "genomics.variants.get" call. Exactly one of *Variant or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Variant.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsGetCall) Header ¶
func (c *VariantsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*VariantsGetCall) IfNoneMatch ¶
func (c *VariantsGetCall) IfNoneMatch(entityTag string) *VariantsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type VariantsImportCall ¶
type VariantsImportCall struct {
// contains filtered or unexported fields
}
func (*VariantsImportCall) Context ¶
func (c *VariantsImportCall) Context(ctx context.Context) *VariantsImportCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsImportCall) Do ¶
func (c *VariantsImportCall) Do(opts ...googleapi.CallOption) (*Operation, error)
Do executes the "genomics.variants.import" call. Exactly one of *Operation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Operation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsImportCall) Header ¶
func (c *VariantsImportCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type VariantsMergeCall ¶
type VariantsMergeCall struct {
// contains filtered or unexported fields
}
func (*VariantsMergeCall) Context ¶
func (c *VariantsMergeCall) Context(ctx context.Context) *VariantsMergeCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsMergeCall) Do ¶
func (c *VariantsMergeCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.variants.merge" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsMergeCall) Header ¶
func (c *VariantsMergeCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type VariantsPatchCall ¶
type VariantsPatchCall struct {
// contains filtered or unexported fields
}
func (*VariantsPatchCall) Context ¶
func (c *VariantsPatchCall) Context(ctx context.Context) *VariantsPatchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsPatchCall) Do ¶
func (c *VariantsPatchCall) Do(opts ...googleapi.CallOption) (*Variant, error)
Do executes the "genomics.variants.patch" call. Exactly one of *Variant or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Variant.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *VariantsPatchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
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 and 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) Context ¶
func (c *VariantsSearchCall) Context(ctx context.Context) *VariantsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsSearchCall) Do ¶
func (c *VariantsSearchCall) Do(opts ...googleapi.CallOption) (*SearchVariantsResponse, error)
Do executes the "genomics.variants.search" call. Exactly one of *SearchVariantsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchVariantsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsSearchCall) Header ¶
func (c *VariantsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*VariantsSearchCall) Pages ¶
func (c *VariantsSearchCall) Pages(ctx context.Context, f func(*SearchVariantsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*VariantsService) Delete ¶
func (r *VariantsService) Delete(variantId string) *VariantsDeleteCall
Delete: Deletes a variant.
For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*VariantsService) Get ¶
func (r *VariantsService) Get(variantId string) *VariantsGetCall
Get: Gets a variant by ID.
For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*VariantsService) Import ¶
func (r *VariantsService) Import(importvariantsrequest *ImportVariantsRequest) *VariantsImportCall
Import: Creates variant data by asynchronously importing the provided information.
For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
The variants for import will be merged with any existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created.
When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.
func (*VariantsService) Merge ¶
func (r *VariantsService) Merge(mergevariantsrequest *MergeVariantsRequest) *VariantsMergeCall
Merge: Merges the given variants with existing variants.
For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created.
When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest.
Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID.
// Existing variant - irrelevant fields trimmed for clarity
{
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
{
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
0,
1
],
}
]
}
// New variant with conflicting call information
{
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
{
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
1,
1
],
}
]
}
The resulting merged variant would overwrite the existing calls with those from the new variant:
{
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
{
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
1,
1
],
}
]
}
This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.
func (*VariantsService) Patch ¶
func (r *VariantsService) Patch(variantId string, variant *Variant) *VariantsPatchCall
Patch: Updates a variant.
For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
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.
For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.searchVariants](https://g ithub.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmet hods.avdl#L126).
type VariantsetsCreateCall ¶
type VariantsetsCreateCall struct {
// contains filtered or unexported fields
}
func (*VariantsetsCreateCall) Context ¶
func (c *VariantsetsCreateCall) Context(ctx context.Context) *VariantsetsCreateCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsetsCreateCall) Do ¶
func (c *VariantsetsCreateCall) Do(opts ...googleapi.CallOption) (*VariantSet, error)
Do executes the "genomics.variantsets.create" call. Exactly one of *VariantSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *VariantSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsetsCreateCall) Header ¶
func (c *VariantsetsCreateCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type VariantsetsDeleteCall ¶
type VariantsetsDeleteCall struct {
// contains filtered or unexported fields
}
func (*VariantsetsDeleteCall) Context ¶
func (c *VariantsetsDeleteCall) Context(ctx context.Context) *VariantsetsDeleteCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsetsDeleteCall) Do ¶
func (c *VariantsetsDeleteCall) Do(opts ...googleapi.CallOption) (*Empty, error)
Do executes the "genomics.variantsets.delete" call. Exactly one of *Empty or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Empty.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsetsDeleteCall) Header ¶
func (c *VariantsetsDeleteCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type VariantsetsExportCall ¶
type VariantsetsExportCall struct {
// contains filtered or unexported fields
}
func (*VariantsetsExportCall) Context ¶
func (c *VariantsetsExportCall) Context(ctx context.Context) *VariantsetsExportCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsetsExportCall) Do ¶
func (c *VariantsetsExportCall) Do(opts ...googleapi.CallOption) (*Operation, error)
Do executes the "genomics.variantsets.export" call. Exactly one of *Operation or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *Operation.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsetsExportCall) Header ¶
func (c *VariantsetsExportCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
type VariantsetsGetCall ¶
type VariantsetsGetCall struct {
// contains filtered or unexported fields
}
func (*VariantsetsGetCall) Context ¶
func (c *VariantsetsGetCall) Context(ctx context.Context) *VariantsetsGetCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsetsGetCall) Do ¶
func (c *VariantsetsGetCall) Do(opts ...googleapi.CallOption) (*VariantSet, error)
Do executes the "genomics.variantsets.get" call. Exactly one of *VariantSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *VariantSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsetsGetCall) Header ¶
func (c *VariantsetsGetCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*VariantsetsGetCall) IfNoneMatch ¶
func (c *VariantsetsGetCall) IfNoneMatch(entityTag string) *VariantsetsGetCall
IfNoneMatch sets the optional parameter which makes the operation fail if the object's ETag matches the given value. This is useful for getting updates only after the object has changed since the last request. Use googleapi.IsNotModified to check whether the response error from Do is the result of In-None-Match.
type VariantsetsPatchCall ¶
type VariantsetsPatchCall struct {
// contains filtered or unexported fields
}
func (*VariantsetsPatchCall) Context ¶
func (c *VariantsetsPatchCall) Context(ctx context.Context) *VariantsetsPatchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsetsPatchCall) Do ¶
func (c *VariantsetsPatchCall) Do(opts ...googleapi.CallOption) (*VariantSet, error)
Do executes the "genomics.variantsets.patch" call. Exactly one of *VariantSet or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *VariantSet.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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) Header ¶
func (c *VariantsetsPatchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*VariantsetsPatchCall) UpdateMask ¶
func (c *VariantsetsPatchCall) UpdateMask(updateMask string) *VariantsetsPatchCall
UpdateMask sets the optional parameter "updateMask": An optional mask specifying which fields to update. Supported fields:
* metadata. * name. * description.
Leaving `updateMask` unset is equivalent to specifying all mutable fields.
type VariantsetsSearchCall ¶
type VariantsetsSearchCall struct {
// contains filtered or unexported fields
}
func (*VariantsetsSearchCall) Context ¶
func (c *VariantsetsSearchCall) Context(ctx context.Context) *VariantsetsSearchCall
Context sets the context to be used in this call's Do method. Any pending HTTP request will be aborted if the provided context is canceled.
func (*VariantsetsSearchCall) Do ¶
func (c *VariantsetsSearchCall) Do(opts ...googleapi.CallOption) (*SearchVariantSetsResponse, error)
Do executes the "genomics.variantsets.search" call. Exactly one of *SearchVariantSetsResponse or error will be non-nil. Any non-2xx status code is an error. Response headers are in either *SearchVariantSetsResponse.ServerResponse.Header or (if a response was returned at all) in error.(*googleapi.Error).Header. Use googleapi.IsNotModified to check whether the returned error was because http.StatusNotModified was returned.
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.
func (*VariantsetsSearchCall) Header ¶
func (c *VariantsetsSearchCall) Header() http.Header
Header returns an http.Header that can be modified by the caller to add HTTP headers to the request.
func (*VariantsetsSearchCall) Pages ¶
func (c *VariantsetsSearchCall) Pages(ctx context.Context, f func(*SearchVariantSetsResponse) error) error
Pages invokes f for each page of results. A non-nil error returned from f will halt the iteration. The provided context supersedes any context provided to the Context method.
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.
For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
The provided variant set must have a valid `datasetId` set - all other fields are optional. Note that the `id` field will be ignored, as this is assigned by the server.
func (*VariantsetsService) Delete ¶
func (r *VariantsetsService) Delete(variantSetId string) *VariantsetsDeleteCall
Delete: Deletes a variant set including all variants, call sets, and calls within. This is not reversible.
For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*VariantsetsService) Export ¶
func (r *VariantsetsService) Export(variantSetId string, exportvariantsetrequest *ExportVariantSetRequest) *VariantsetsExportCall
Export: Exports variant set data to an external destination.
For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*VariantsetsService) Get ¶
func (r *VariantsetsService) Get(variantSetId string) *VariantsetsGetCall
Get: Gets a variant set by ID.
For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*VariantsetsService) Patch ¶
func (r *VariantsetsService) Patch(variantSetId string, variantset *VariantSet) *VariantsetsPatchCall
Patch: Updates a variant set using patch semantics.
For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
func (*VariantsetsService) Search ¶
func (r *VariantsetsService) Search(searchvariantsetsrequest *SearchVariantSetsRequest) *VariantsetsSearchCall
Search: Returns a list of all variant sets matching search criteria.
For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-goo gle-genomics)
Implements [GlobalAllianceApi.searchVariantSets](https: //github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variant methods.avdl#L49).