Enum value maps for AnnotationType.
var (
AnnotationType_name = map[int32]string{
0: "ANNOTATION_TYPE_UNSPECIFIED",
1: "GENERIC",
2: "VARIANT",
3: "GENE",
4: "TRANSCRIPT",
}
AnnotationType_value = map[string]int32{
"ANNOTATION_TYPE_UNSPECIFIED": 0,
"GENERIC": 1,
"VARIANT": 2,
"GENE": 3,
"TRANSCRIPT": 4,
}
)
Enum value maps for VariantAnnotation_Type.
var (
VariantAnnotation_Type_name = map[int32]string{
0: "TYPE_UNSPECIFIED",
1: "TYPE_OTHER",
2: "INSERTION",
3: "DELETION",
4: "SUBSTITUTION",
5: "SNP",
6: "STRUCTURAL",
7: "CNV",
}
VariantAnnotation_Type_value = map[string]int32{
"TYPE_UNSPECIFIED": 0,
"TYPE_OTHER": 1,
"INSERTION": 2,
"DELETION": 3,
"SUBSTITUTION": 4,
"SNP": 5,
"STRUCTURAL": 6,
"CNV": 7,
}
)
Enum value maps for VariantAnnotation_Effect.
var (
VariantAnnotation_Effect_name = map[int32]string{
0: "EFFECT_UNSPECIFIED",
1: "EFFECT_OTHER",
2: "FRAMESHIFT",
3: "FRAME_PRESERVING_INDEL",
4: "SYNONYMOUS_SNP",
5: "NONSYNONYMOUS_SNP",
6: "STOP_GAIN",
7: "STOP_LOSS",
8: "SPLICE_SITE_DISRUPTION",
}
VariantAnnotation_Effect_value = map[string]int32{
"EFFECT_UNSPECIFIED": 0,
"EFFECT_OTHER": 1,
"FRAMESHIFT": 2,
"FRAME_PRESERVING_INDEL": 3,
"SYNONYMOUS_SNP": 4,
"NONSYNONYMOUS_SNP": 5,
"STOP_GAIN": 6,
"STOP_LOSS": 7,
"SPLICE_SITE_DISRUPTION": 8,
}
)
Enum value maps for VariantAnnotation_ClinicalSignificance.
var (
VariantAnnotation_ClinicalSignificance_name = map[int32]string{
0: "CLINICAL_SIGNIFICANCE_UNSPECIFIED",
1: "CLINICAL_SIGNIFICANCE_OTHER",
2: "UNCERTAIN",
3: "BENIGN",
4: "LIKELY_BENIGN",
5: "LIKELY_PATHOGENIC",
6: "PATHOGENIC",
7: "DRUG_RESPONSE",
8: "HISTOCOMPATIBILITY",
9: "CONFERS_SENSITIVITY",
10: "RISK_FACTOR",
11: "ASSOCIATION",
12: "PROTECTIVE",
13: "MULTIPLE_REPORTED",
}
VariantAnnotation_ClinicalSignificance_value = map[string]int32{
"CLINICAL_SIGNIFICANCE_UNSPECIFIED": 0,
"CLINICAL_SIGNIFICANCE_OTHER": 1,
"UNCERTAIN": 2,
"BENIGN": 3,
"LIKELY_BENIGN": 4,
"LIKELY_PATHOGENIC": 5,
"PATHOGENIC": 6,
"DRUG_RESPONSE": 7,
"HISTOCOMPATIBILITY": 8,
"CONFERS_SENSITIVITY": 9,
"RISK_FACTOR": 10,
"ASSOCIATION": 11,
"PROTECTIVE": 12,
"MULTIPLE_REPORTED": 13,
}
)
Enum value maps for CigarUnit_Operation.
var (
CigarUnit_Operation_name = map[int32]string{
0: "OPERATION_UNSPECIFIED",
1: "ALIGNMENT_MATCH",
2: "INSERT",
3: "DELETE",
4: "SKIP",
5: "CLIP_SOFT",
6: "CLIP_HARD",
7: "PAD",
8: "SEQUENCE_MATCH",
9: "SEQUENCE_MISMATCH",
}
CigarUnit_Operation_value = map[string]int32{
"OPERATION_UNSPECIFIED": 0,
"ALIGNMENT_MATCH": 1,
"INSERT": 2,
"DELETE": 3,
"SKIP": 4,
"CLIP_SOFT": 5,
"CLIP_HARD": 6,
"PAD": 7,
"SEQUENCE_MATCH": 8,
"SEQUENCE_MISMATCH": 9,
}
)
Enum value maps for ImportReadGroupSetsRequest_PartitionStrategy.
var (
ImportReadGroupSetsRequest_PartitionStrategy_name = map[int32]string{
0: "PARTITION_STRATEGY_UNSPECIFIED",
1: "PER_FILE_PER_SAMPLE",
2: "MERGE_ALL",
}
ImportReadGroupSetsRequest_PartitionStrategy_value = map[string]int32{
"PARTITION_STRATEGY_UNSPECIFIED": 0,
"PER_FILE_PER_SAMPLE": 1,
"MERGE_ALL": 2,
}
)
Enum value maps for InfoMergeOperation.
var (
InfoMergeOperation_name = map[int32]string{
0: "INFO_MERGE_OPERATION_UNSPECIFIED",
1: "IGNORE_NEW",
2: "MOVE_TO_CALLS",
}
InfoMergeOperation_value = map[string]int32{
"INFO_MERGE_OPERATION_UNSPECIFIED": 0,
"IGNORE_NEW": 1,
"MOVE_TO_CALLS": 2,
}
)
Enum value maps for VariantSetMetadata_Type.
var (
VariantSetMetadata_Type_name = map[int32]string{
0: "TYPE_UNSPECIFIED",
1: "INTEGER",
2: "FLOAT",
3: "FLAG",
4: "CHARACTER",
5: "STRING",
}
VariantSetMetadata_Type_value = map[string]int32{
"TYPE_UNSPECIFIED": 0,
"INTEGER": 1,
"FLOAT": 2,
"FLAG": 3,
"CHARACTER": 4,
"STRING": 5,
}
)
Enum value maps for ImportVariantsRequest_Format.
var (
ImportVariantsRequest_Format_name = map[int32]string{
0: "FORMAT_UNSPECIFIED",
1: "FORMAT_VCF",
2: "FORMAT_COMPLETE_GENOMICS",
}
ImportVariantsRequest_Format_value = map[string]int32{
"FORMAT_UNSPECIFIED": 0,
"FORMAT_VCF": 1,
"FORMAT_COMPLETE_GENOMICS": 2,
}
)
Enum value maps for ExportVariantSetRequest_Format.
var (
ExportVariantSetRequest_Format_name = map[int32]string{
0: "FORMAT_UNSPECIFIED",
1: "FORMAT_BIGQUERY",
}
ExportVariantSetRequest_Format_value = map[string]int32{
"FORMAT_UNSPECIFIED": 0,
"FORMAT_BIGQUERY": 1,
}
)
var File_google_genomics_v1_annotations_proto protoreflect.FileDescriptor
var File_google_genomics_v1_cigar_proto protoreflect.FileDescriptor
var File_google_genomics_v1_datasets_proto protoreflect.FileDescriptor
var File_google_genomics_v1_operations_proto protoreflect.FileDescriptor
var File_google_genomics_v1_position_proto protoreflect.FileDescriptor
var File_google_genomics_v1_range_proto protoreflect.FileDescriptor
var File_google_genomics_v1_readalignment_proto protoreflect.FileDescriptor
var File_google_genomics_v1_readgroup_proto protoreflect.FileDescriptor
var File_google_genomics_v1_readgroupset_proto protoreflect.FileDescriptor
var File_google_genomics_v1_reads_proto protoreflect.FileDescriptor
var File_google_genomics_v1_references_proto protoreflect.FileDescriptor
var File_google_genomics_v1_variants_proto protoreflect.FileDescriptor
func RegisterAnnotationServiceV1Server(s *grpc.Server, srv AnnotationServiceV1Server)
func RegisterDatasetServiceV1Server(s *grpc.Server, srv DatasetServiceV1Server)
func RegisterReadServiceV1Server(s *grpc.Server, srv ReadServiceV1Server)
func RegisterReferenceServiceV1Server(s *grpc.Server, srv ReferenceServiceV1Server)
func RegisterStreamingReadServiceServer(s *grpc.Server, srv StreamingReadServiceServer)
func RegisterStreamingVariantServiceServer(s *grpc.Server, srv StreamingVariantServiceServer)
func RegisterVariantServiceV1Server(s *grpc.Server, srv VariantServiceV1Server)
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 {
// The server-generated annotation ID, unique across all annotations.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The annotation set to which this annotation belongs.
AnnotationSetId string `protobuf:"bytes,2,opt,name=annotation_set_id,json=annotationSetId,proto3" json:"annotation_set_id,omitempty"`
// The display name of this annotation.
Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,omitempty"`
// The ID of the Google Genomics reference associated with this range.
ReferenceId string `protobuf:"bytes,4,opt,name=reference_id,json=referenceId,proto3" json:"reference_id,omitempty"`
// The display name corresponding to the reference specified by
// `referenceId`, for example `chr1`, `1`, or `chrX`.
ReferenceName string `protobuf:"bytes,5,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive.
Start int64 `protobuf:"varint,6,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive.
End int64 `protobuf:"varint,7,opt,name=end,proto3" json:"end,omitempty"`
// 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 `protobuf:"varint,8,opt,name=reverse_strand,json=reverseStrand,proto3" json:"reverse_strand,omitempty"`
// The data type for this annotation. Must match the containing annotation
// set's type.
Type AnnotationType `protobuf:"varint,9,opt,name=type,proto3,enum=google.genomics.v1.AnnotationType" json:"type,omitempty"`
// Types that are assignable to Value:
//
// *Annotation_Variant
// *Annotation_Transcript
Value isAnnotation_Value `protobuf_oneof:"value"`
// 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]*structpb.ListValue `protobuf:"bytes,12,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*Annotation) Descriptor() ([]byte, []int)
Deprecated: Use Annotation.ProtoReflect.Descriptor instead.
func (x *Annotation) GetAnnotationSetId() string
func (x *Annotation) GetEnd() int64
func (x *Annotation) GetId() string
func (x *Annotation) GetInfo() map[string]*structpb.ListValue
func (x *Annotation) GetName() string
func (x *Annotation) GetReferenceId() string
func (x *Annotation) GetReferenceName() string
func (x *Annotation) GetReverseStrand() bool
func (x *Annotation) GetStart() int64
func (x *Annotation) GetTranscript() *Transcript
func (x *Annotation) GetType() AnnotationType
func (m *Annotation) GetValue() isAnnotation_Value
func (x *Annotation) GetVariant() *VariantAnnotation
func (*Annotation) ProtoMessage()
func (x *Annotation) ProtoReflect() protoreflect.Message
func (x *Annotation) Reset()
func (x *Annotation) String() string
AnnotationServiceV1Client is the client API for AnnotationServiceV1 service.
For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.
type AnnotationServiceV1Client interface {
// Creates a new annotation set. Caller must have WRITE permission for the
// associated dataset.
//
// The following fields are required:
//
// - [datasetId][google.genomics.v1.AnnotationSet.dataset_id]
// - [referenceSetId][google.genomics.v1.AnnotationSet.reference_set_id]
//
// All other fields may be optionally specified, unless documented as being
// server-generated (for example, the `id` field).
CreateAnnotationSet(ctx context.Context, in *CreateAnnotationSetRequest, opts ...grpc.CallOption) (*AnnotationSet, error)
// Gets an annotation set. Caller must have READ permission for
// the associated dataset.
GetAnnotationSet(ctx context.Context, in *GetAnnotationSetRequest, opts ...grpc.CallOption) (*AnnotationSet, error)
// 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.
UpdateAnnotationSet(ctx context.Context, in *UpdateAnnotationSetRequest, opts ...grpc.CallOption) (*AnnotationSet, error)
// Deletes an annotation set. Caller must have WRITE permission
// for the associated annotation set.
DeleteAnnotationSet(ctx context.Context, in *DeleteAnnotationSetRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// 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.
SearchAnnotationSets(ctx context.Context, in *SearchAnnotationSetsRequest, opts ...grpc.CallOption) (*SearchAnnotationSetsResponse, error)
// Creates a new annotation. Caller must have WRITE permission
// for the associated annotation set.
//
// The following fields are required:
//
// - [annotationSetId][google.genomics.v1.Annotation.annotation_set_id]
// - [referenceName][google.genomics.v1.Annotation.reference_name] or
// [referenceId][google.genomics.v1.Annotation.reference_id]
//
// ### Transcripts
//
// For annotations of type TRANSCRIPT, the following fields of
// [transcript][google.genomics.v1.Annotation.transcript] must be provided:
//
// * [exons.start][google.genomics.v1.Transcript.Exon.start]
// * [exons.end][google.genomics.v1.Transcript.Exon.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][google.genomics.v1.Annotation]
// for additional restrictions on each field.
CreateAnnotation(ctx context.Context, in *CreateAnnotationRequest, opts ...grpc.CallOption) (*Annotation, error)
// 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][google.genomics.v1.AnnotationServiceV1.CreateAnnotation].
BatchCreateAnnotations(ctx context.Context, in *BatchCreateAnnotationsRequest, opts ...grpc.CallOption) (*BatchCreateAnnotationsResponse, error)
// Gets an annotation. Caller must have READ permission
// for the associated annotation set.
GetAnnotation(ctx context.Context, in *GetAnnotationRequest, opts ...grpc.CallOption) (*Annotation, error)
// Updates an annotation. Caller must have
// WRITE permission for the associated dataset.
UpdateAnnotation(ctx context.Context, in *UpdateAnnotationRequest, opts ...grpc.CallOption) (*Annotation, error)
// Deletes an annotation. Caller must have WRITE permission for
// the associated annotation set.
DeleteAnnotation(ctx context.Context, in *DeleteAnnotationRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// 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.
SearchAnnotations(ctx context.Context, in *SearchAnnotationsRequest, opts ...grpc.CallOption) (*SearchAnnotationsResponse, error)
}
func NewAnnotationServiceV1Client(cc grpc.ClientConnInterface) AnnotationServiceV1Client
AnnotationServiceV1Server is the server API for AnnotationServiceV1 service.
type AnnotationServiceV1Server interface {
// Creates a new annotation set. Caller must have WRITE permission for the
// associated dataset.
//
// The following fields are required:
//
// - [datasetId][google.genomics.v1.AnnotationSet.dataset_id]
// - [referenceSetId][google.genomics.v1.AnnotationSet.reference_set_id]
//
// All other fields may be optionally specified, unless documented as being
// server-generated (for example, the `id` field).
CreateAnnotationSet(context.Context, *CreateAnnotationSetRequest) (*AnnotationSet, error)
// Gets an annotation set. Caller must have READ permission for
// the associated dataset.
GetAnnotationSet(context.Context, *GetAnnotationSetRequest) (*AnnotationSet, error)
// 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.
UpdateAnnotationSet(context.Context, *UpdateAnnotationSetRequest) (*AnnotationSet, error)
// Deletes an annotation set. Caller must have WRITE permission
// for the associated annotation set.
DeleteAnnotationSet(context.Context, *DeleteAnnotationSetRequest) (*emptypb.Empty, error)
// 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.
SearchAnnotationSets(context.Context, *SearchAnnotationSetsRequest) (*SearchAnnotationSetsResponse, error)
// Creates a new annotation. Caller must have WRITE permission
// for the associated annotation set.
//
// The following fields are required:
//
// - [annotationSetId][google.genomics.v1.Annotation.annotation_set_id]
// - [referenceName][google.genomics.v1.Annotation.reference_name] or
// [referenceId][google.genomics.v1.Annotation.reference_id]
//
// ### Transcripts
//
// For annotations of type TRANSCRIPT, the following fields of
// [transcript][google.genomics.v1.Annotation.transcript] must be provided:
//
// * [exons.start][google.genomics.v1.Transcript.Exon.start]
// * [exons.end][google.genomics.v1.Transcript.Exon.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][google.genomics.v1.Annotation]
// for additional restrictions on each field.
CreateAnnotation(context.Context, *CreateAnnotationRequest) (*Annotation, error)
// 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][google.genomics.v1.AnnotationServiceV1.CreateAnnotation].
BatchCreateAnnotations(context.Context, *BatchCreateAnnotationsRequest) (*BatchCreateAnnotationsResponse, error)
// Gets an annotation. Caller must have READ permission
// for the associated annotation set.
GetAnnotation(context.Context, *GetAnnotationRequest) (*Annotation, error)
// Updates an annotation. Caller must have
// WRITE permission for the associated dataset.
UpdateAnnotation(context.Context, *UpdateAnnotationRequest) (*Annotation, error)
// Deletes an annotation. Caller must have WRITE permission for
// the associated annotation set.
DeleteAnnotation(context.Context, *DeleteAnnotationRequest) (*emptypb.Empty, error)
// 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.
SearchAnnotations(context.Context, *SearchAnnotationsRequest) (*SearchAnnotationsResponse, error)
}
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 {
// The server-generated annotation set ID, unique across all annotation sets.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The dataset to which this annotation set belongs.
DatasetId string `protobuf:"bytes,2,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// The ID of the reference set that defines the coordinate space for this
// set's annotations.
ReferenceSetId string `protobuf:"bytes,3,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// The display name for this annotation set.
Name string `protobuf:"bytes,4,opt,name=name,proto3" json:"name,omitempty"`
// The source URI describing the file from which this annotation set was
// generated, if any.
SourceUri string `protobuf:"bytes,5,opt,name=source_uri,json=sourceUri,proto3" json:"source_uri,omitempty"`
// The type of annotations contained within this set.
Type AnnotationType `protobuf:"varint,6,opt,name=type,proto3,enum=google.genomics.v1.AnnotationType" json:"type,omitempty"`
// 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]*structpb.ListValue `protobuf:"bytes,17,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*AnnotationSet) Descriptor() ([]byte, []int)
Deprecated: Use AnnotationSet.ProtoReflect.Descriptor instead.
func (x *AnnotationSet) GetDatasetId() string
func (x *AnnotationSet) GetId() string
func (x *AnnotationSet) GetInfo() map[string]*structpb.ListValue
func (x *AnnotationSet) GetName() string
func (x *AnnotationSet) GetReferenceSetId() string
func (x *AnnotationSet) GetSourceUri() string
func (x *AnnotationSet) GetType() AnnotationType
func (*AnnotationSet) ProtoMessage()
func (x *AnnotationSet) ProtoReflect() protoreflect.Message
func (x *AnnotationSet) Reset()
func (x *AnnotationSet) String() string
When an Annotation[google.genomics.v1.Annotation] or AnnotationSet[google.genomics.v1.AnnotationSet] is created, if `type` is not specified it will be set to `GENERIC`.
type AnnotationType int32
const (
AnnotationType_ANNOTATION_TYPE_UNSPECIFIED AnnotationType = 0
// A `GENERIC` annotation type should be used when no other annotation
// type will suffice. This represents an untyped annotation of the reference
// genome.
AnnotationType_GENERIC AnnotationType = 1
// A `VARIANT` annotation type.
AnnotationType_VARIANT AnnotationType = 2
// 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.
AnnotationType_GENE AnnotationType = 3
// A `TRANSCRIPT` annotation type represents the assertion that a
// particular region of the reference genome may be transcribed as RNA.
AnnotationType_TRANSCRIPT AnnotationType = 4
)
func (AnnotationType) Descriptor() protoreflect.EnumDescriptor
func (x AnnotationType) Enum() *AnnotationType
func (AnnotationType) EnumDescriptor() ([]byte, []int)
Deprecated: Use AnnotationType.Descriptor instead.
func (x AnnotationType) Number() protoreflect.EnumNumber
func (x AnnotationType) String() string
func (AnnotationType) Type() protoreflect.EnumType
type Annotation_Transcript struct {
// 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 `protobuf:"bytes,11,opt,name=transcript,proto3,oneof"`
}
type Annotation_Variant struct {
// 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 `protobuf:"bytes,10,opt,name=variant,proto3,oneof"`
}
type BatchCreateAnnotationsRequest struct {
// The annotations to be created. At most 4096 can be specified in a single
// request.
Annotations []*Annotation `protobuf:"bytes,1,rep,name=annotations,proto3" json:"annotations,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=request_id,json=requestId,proto3" json:"request_id,omitempty"`
// contains filtered or unexported fields
}
func (*BatchCreateAnnotationsRequest) Descriptor() ([]byte, []int)
Deprecated: Use BatchCreateAnnotationsRequest.ProtoReflect.Descriptor instead.
func (x *BatchCreateAnnotationsRequest) GetAnnotations() []*Annotation
func (x *BatchCreateAnnotationsRequest) GetRequestId() string
func (*BatchCreateAnnotationsRequest) ProtoMessage()
func (x *BatchCreateAnnotationsRequest) ProtoReflect() protoreflect.Message
func (x *BatchCreateAnnotationsRequest) Reset()
func (x *BatchCreateAnnotationsRequest) String() string
type BatchCreateAnnotationsResponse struct {
// The resulting per-annotation entries, ordered consistently with the
// original request.
Entries []*BatchCreateAnnotationsResponse_Entry `protobuf:"bytes,1,rep,name=entries,proto3" json:"entries,omitempty"`
// contains filtered or unexported fields
}
func (*BatchCreateAnnotationsResponse) Descriptor() ([]byte, []int)
Deprecated: Use BatchCreateAnnotationsResponse.ProtoReflect.Descriptor instead.
func (x *BatchCreateAnnotationsResponse) GetEntries() []*BatchCreateAnnotationsResponse_Entry
func (*BatchCreateAnnotationsResponse) ProtoMessage()
func (x *BatchCreateAnnotationsResponse) ProtoReflect() protoreflect.Message
func (x *BatchCreateAnnotationsResponse) Reset()
func (x *BatchCreateAnnotationsResponse) String() string
type BatchCreateAnnotationsResponse_Entry struct {
// The creation status.
Status *status.Status `protobuf:"bytes,1,opt,name=status,proto3" json:"status,omitempty"`
// The created annotation, if creation was successful.
Annotation *Annotation `protobuf:"bytes,2,opt,name=annotation,proto3" json:"annotation,omitempty"`
// contains filtered or unexported fields
}
func (*BatchCreateAnnotationsResponse_Entry) Descriptor() ([]byte, []int)
Deprecated: Use BatchCreateAnnotationsResponse_Entry.ProtoReflect.Descriptor instead.
func (x *BatchCreateAnnotationsResponse_Entry) GetAnnotation() *Annotation
func (x *BatchCreateAnnotationsResponse_Entry) GetStatus() *status.Status
func (*BatchCreateAnnotationsResponse_Entry) ProtoMessage()
func (x *BatchCreateAnnotationsResponse_Entry) ProtoReflect() protoreflect.Message
func (x *BatchCreateAnnotationsResponse_Entry) Reset()
func (x *BatchCreateAnnotationsResponse_Entry) String() string
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-google-genomics)
type CallSet struct {
// The server-generated call set ID, unique across all call sets.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The call set name.
Name string `protobuf:"bytes,2,opt,name=name,proto3" json:"name,omitempty"`
// The sample ID this call set corresponds to.
SampleId string `protobuf:"bytes,7,opt,name=sample_id,json=sampleId,proto3" json:"sample_id,omitempty"`
// The IDs of the variant sets this call set belongs to. This field must
// have exactly length one, as a call set belongs to a single variant set.
// This field is repeated for compatibility with the
// [GA4GH 0.5.1
// API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76).
VariantSetIds []string `protobuf:"bytes,6,rep,name=variant_set_ids,json=variantSetIds,proto3" json:"variant_set_ids,omitempty"`
// The date this call set was created in milliseconds from the epoch.
Created int64 `protobuf:"varint,5,opt,name=created,proto3" json:"created,omitempty"`
// 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]*structpb.ListValue `protobuf:"bytes,4,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*CallSet) Descriptor() ([]byte, []int)
Deprecated: Use CallSet.ProtoReflect.Descriptor instead.
func (x *CallSet) GetCreated() int64
func (x *CallSet) GetId() string
func (x *CallSet) GetInfo() map[string]*structpb.ListValue
func (x *CallSet) GetName() string
func (x *CallSet) GetSampleId() string
func (x *CallSet) GetVariantSetIds() []string
func (*CallSet) ProtoMessage()
func (x *CallSet) ProtoReflect() protoreflect.Message
func (x *CallSet) Reset()
func (x *CallSet) String() string
A single CIGAR operation.
type CigarUnit struct {
Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,proto3,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"`
// The number of genomic bases that the operation runs for. Required.
OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength,proto3" json:"operation_length,omitempty"`
// `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 `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence,proto3" json:"reference_sequence,omitempty"`
// contains filtered or unexported fields
}
func (*CigarUnit) Descriptor() ([]byte, []int)
Deprecated: Use CigarUnit.ProtoReflect.Descriptor instead.
func (x *CigarUnit) GetOperation() CigarUnit_Operation
func (x *CigarUnit) GetOperationLength() int64
func (x *CigarUnit) GetReferenceSequence() string
func (*CigarUnit) ProtoMessage()
func (x *CigarUnit) ProtoReflect() protoreflect.Message
func (x *CigarUnit) Reset()
func (x *CigarUnit) String() string
Describes the different types of CIGAR alignment operations that exist. Used wherever CIGAR alignments are used.
type CigarUnit_Operation int32
const (
CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0
// 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`.
CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1
// The insert operator indicates that the read contains evidence of bases
// being inserted into the reference. This operator is equivalent to SAM's
// `I`.
CigarUnit_INSERT CigarUnit_Operation = 2
// The delete operator indicates that the read contains evidence of bases
// being deleted from the reference. This operator is equivalent to SAM's
// `D`.
CigarUnit_DELETE CigarUnit_Operation = 3
// 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`.
CigarUnit_SKIP CigarUnit_Operation = 4
// 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.
CigarUnit_CLIP_SOFT CigarUnit_Operation = 5
// 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`.
CigarUnit_CLIP_HARD CigarUnit_Operation = 6
// The pad operator indicates that there is padding in an alignment. This
// operator is equivalent to SAM's `P`.
CigarUnit_PAD CigarUnit_Operation = 7
// This operator indicates that this portion of the aligned sequence exactly
// matches the reference. This operator is equivalent to SAM's `=`.
CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8
// 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`.
CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9
)
func (CigarUnit_Operation) Descriptor() protoreflect.EnumDescriptor
func (x CigarUnit_Operation) Enum() *CigarUnit_Operation
func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int)
Deprecated: Use CigarUnit_Operation.Descriptor instead.
func (x CigarUnit_Operation) Number() protoreflect.EnumNumber
func (x CigarUnit_Operation) String() string
func (CigarUnit_Operation) Type() protoreflect.EnumType
A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.
type CoverageBucket struct {
// The genomic coordinate range spanned by this bucket.
Range *Range `protobuf:"bytes,1,opt,name=range,proto3" json:"range,omitempty"`
// The average number of reads which are aligned to each individual
// reference base in this bucket.
MeanCoverage float32 `protobuf:"fixed32,2,opt,name=mean_coverage,json=meanCoverage,proto3" json:"mean_coverage,omitempty"`
// contains filtered or unexported fields
}
func (*CoverageBucket) Descriptor() ([]byte, []int)
Deprecated: Use CoverageBucket.ProtoReflect.Descriptor instead.
func (x *CoverageBucket) GetMeanCoverage() float32
func (x *CoverageBucket) GetRange() *Range
func (*CoverageBucket) ProtoMessage()
func (x *CoverageBucket) ProtoReflect() protoreflect.Message
func (x *CoverageBucket) Reset()
func (x *CoverageBucket) String() string
type CreateAnnotationRequest struct {
// The annotation to be created.
Annotation *Annotation `protobuf:"bytes,1,opt,name=annotation,proto3" json:"annotation,omitempty"`
// contains filtered or unexported fields
}
func (*CreateAnnotationRequest) Descriptor() ([]byte, []int)
Deprecated: Use CreateAnnotationRequest.ProtoReflect.Descriptor instead.
func (x *CreateAnnotationRequest) GetAnnotation() *Annotation
func (*CreateAnnotationRequest) ProtoMessage()
func (x *CreateAnnotationRequest) ProtoReflect() protoreflect.Message
func (x *CreateAnnotationRequest) Reset()
func (x *CreateAnnotationRequest) String() string
type CreateAnnotationSetRequest struct {
// The annotation set to create.
AnnotationSet *AnnotationSet `protobuf:"bytes,1,opt,name=annotation_set,json=annotationSet,proto3" json:"annotation_set,omitempty"`
// contains filtered or unexported fields
}
func (*CreateAnnotationSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use CreateAnnotationSetRequest.ProtoReflect.Descriptor instead.
func (x *CreateAnnotationSetRequest) GetAnnotationSet() *AnnotationSet
func (*CreateAnnotationSetRequest) ProtoMessage()
func (x *CreateAnnotationSetRequest) ProtoReflect() protoreflect.Message
func (x *CreateAnnotationSetRequest) Reset()
func (x *CreateAnnotationSetRequest) String() string
type CreateCallSetRequest struct {
// The call set to be created.
CallSet *CallSet `protobuf:"bytes,1,opt,name=call_set,json=callSet,proto3" json:"call_set,omitempty"`
// contains filtered or unexported fields
}
func (*CreateCallSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use CreateCallSetRequest.ProtoReflect.Descriptor instead.
func (x *CreateCallSetRequest) GetCallSet() *CallSet
func (*CreateCallSetRequest) ProtoMessage()
func (x *CreateCallSetRequest) ProtoReflect() protoreflect.Message
func (x *CreateCallSetRequest) Reset()
func (x *CreateCallSetRequest) String() string
type CreateDatasetRequest struct {
// The dataset to be created. Must contain projectId and name.
Dataset *Dataset `protobuf:"bytes,1,opt,name=dataset,proto3" json:"dataset,omitempty"`
// contains filtered or unexported fields
}
func (*CreateDatasetRequest) Descriptor() ([]byte, []int)
Deprecated: Use CreateDatasetRequest.ProtoReflect.Descriptor instead.
func (x *CreateDatasetRequest) GetDataset() *Dataset
func (*CreateDatasetRequest) ProtoMessage()
func (x *CreateDatasetRequest) ProtoReflect() protoreflect.Message
func (x *CreateDatasetRequest) Reset()
func (x *CreateDatasetRequest) String() string
type CreateVariantRequest struct {
// The variant to be created.
Variant *Variant `protobuf:"bytes,1,opt,name=variant,proto3" json:"variant,omitempty"`
// contains filtered or unexported fields
}
func (*CreateVariantRequest) Descriptor() ([]byte, []int)
Deprecated: Use CreateVariantRequest.ProtoReflect.Descriptor instead.
func (x *CreateVariantRequest) GetVariant() *Variant
func (*CreateVariantRequest) ProtoMessage()
func (x *CreateVariantRequest) ProtoReflect() protoreflect.Message
func (x *CreateVariantRequest) Reset()
func (x *CreateVariantRequest) String() string
The CreateVariantSet request
type CreateVariantSetRequest struct {
// Required. The variant set to be created. Must have a valid `datasetId`.
VariantSet *VariantSet `protobuf:"bytes,1,opt,name=variant_set,json=variantSet,proto3" json:"variant_set,omitempty"`
// contains filtered or unexported fields
}
func (*CreateVariantSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use CreateVariantSetRequest.ProtoReflect.Descriptor instead.
func (x *CreateVariantSetRequest) GetVariantSet() *VariantSet
func (*CreateVariantSetRequest) ProtoMessage()
func (x *CreateVariantSetRequest) ProtoReflect() protoreflect.Message
func (x *CreateVariantSetRequest) Reset()
func (x *CreateVariantSetRequest) String() string
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-google-genomics)
type Dataset struct {
// The server-generated dataset ID, unique across all datasets.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The Google Cloud project ID that this dataset belongs to.
ProjectId string `protobuf:"bytes,2,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// The dataset name.
Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,omitempty"`
// The time this dataset was created, in seconds from the epoch.
CreateTime *timestamppb.Timestamp `protobuf:"bytes,4,opt,name=create_time,json=createTime,proto3" json:"create_time,omitempty"`
// contains filtered or unexported fields
}
func (*Dataset) Descriptor() ([]byte, []int)
Deprecated: Use Dataset.ProtoReflect.Descriptor instead.
func (x *Dataset) GetCreateTime() *timestamppb.Timestamp
func (x *Dataset) GetId() string
func (x *Dataset) GetName() string
func (x *Dataset) GetProjectId() string
func (*Dataset) ProtoMessage()
func (x *Dataset) ProtoReflect() protoreflect.Message
func (x *Dataset) Reset()
func (x *Dataset) String() string
DatasetServiceV1Client is the client API for DatasetServiceV1 service.
For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.
type DatasetServiceV1Client interface {
// Lists datasets within a project.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
ListDatasets(ctx context.Context, in *ListDatasetsRequest, opts ...grpc.CallOption) (*ListDatasetsResponse, error)
// Creates a new dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateDataset(ctx context.Context, in *CreateDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// Gets a dataset by ID.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetDataset(ctx context.Context, in *GetDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// Updates a dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateDataset(ctx context.Context, in *UpdateDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// 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][google.genomics.v1.DatasetServiceV1.UndeleteDataset]
// operation.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteDataset(ctx context.Context, in *DeleteDatasetRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// Undeletes a dataset by restoring a dataset which was deleted via this API.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This operation is only possible for a week after the deletion occurred.
UndeleteDataset(ctx context.Context, in *UndeleteDatasetRequest, opts ...grpc.CallOption) (*Dataset, error)
// Sets the access control policy on the specified dataset. Replaces any
// existing policy.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
// Policy</a> for more information.
SetIamPolicy(ctx context.Context, in *iampb.SetIamPolicyRequest, opts ...grpc.CallOption) (*iampb.Policy, error)
// Gets the access control policy for the dataset. This is empty if the
// policy or resource does not exist.
//
// See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
// Policy</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetIamPolicy(ctx context.Context, in *iampb.GetIamPolicyRequest, opts ...grpc.CallOption) (*iampb.Policy, error)
// Returns permissions that a caller has on the specified resource.
// See <a href="/iam/docs/managing-policies#testing_permissions">Testing
// Permissions</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
TestIamPermissions(ctx context.Context, in *iampb.TestIamPermissionsRequest, opts ...grpc.CallOption) (*iampb.TestIamPermissionsResponse, error)
}
func NewDatasetServiceV1Client(cc grpc.ClientConnInterface) DatasetServiceV1Client
DatasetServiceV1Server is the server API for DatasetServiceV1 service.
type DatasetServiceV1Server interface {
// Lists datasets within a project.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
ListDatasets(context.Context, *ListDatasetsRequest) (*ListDatasetsResponse, error)
// Creates a new dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateDataset(context.Context, *CreateDatasetRequest) (*Dataset, error)
// Gets a dataset by ID.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetDataset(context.Context, *GetDatasetRequest) (*Dataset, error)
// Updates a dataset.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateDataset(context.Context, *UpdateDatasetRequest) (*Dataset, error)
// 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][google.genomics.v1.DatasetServiceV1.UndeleteDataset]
// operation.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteDataset(context.Context, *DeleteDatasetRequest) (*emptypb.Empty, error)
// Undeletes a dataset by restoring a dataset which was deleted via this API.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This operation is only possible for a week after the deletion occurred.
UndeleteDataset(context.Context, *UndeleteDatasetRequest) (*Dataset, error)
// Sets the access control policy on the specified dataset. Replaces any
// existing policy.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
// Policy</a> for more information.
SetIamPolicy(context.Context, *iampb.SetIamPolicyRequest) (*iampb.Policy, error)
// Gets the access control policy for the dataset. This is empty if the
// policy or resource does not exist.
//
// See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
// Policy</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetIamPolicy(context.Context, *iampb.GetIamPolicyRequest) (*iampb.Policy, error)
// Returns permissions that a caller has on the specified resource.
// See <a href="/iam/docs/managing-policies#testing_permissions">Testing
// Permissions</a> for more information.
//
// For the definitions of datasets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
TestIamPermissions(context.Context, *iampb.TestIamPermissionsRequest) (*iampb.TestIamPermissionsResponse, error)
}
type DeleteAnnotationRequest struct {
// The ID of the annotation to be deleted.
AnnotationId string `protobuf:"bytes,1,opt,name=annotation_id,json=annotationId,proto3" json:"annotation_id,omitempty"`
// contains filtered or unexported fields
}
func (*DeleteAnnotationRequest) Descriptor() ([]byte, []int)
Deprecated: Use DeleteAnnotationRequest.ProtoReflect.Descriptor instead.
func (x *DeleteAnnotationRequest) GetAnnotationId() string
func (*DeleteAnnotationRequest) ProtoMessage()
func (x *DeleteAnnotationRequest) ProtoReflect() protoreflect.Message
func (x *DeleteAnnotationRequest) Reset()
func (x *DeleteAnnotationRequest) String() string
type DeleteAnnotationSetRequest struct {
// The ID of the annotation set to be deleted.
AnnotationSetId string `protobuf:"bytes,1,opt,name=annotation_set_id,json=annotationSetId,proto3" json:"annotation_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*DeleteAnnotationSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use DeleteAnnotationSetRequest.ProtoReflect.Descriptor instead.
func (x *DeleteAnnotationSetRequest) GetAnnotationSetId() string
func (*DeleteAnnotationSetRequest) ProtoMessage()
func (x *DeleteAnnotationSetRequest) ProtoReflect() protoreflect.Message
func (x *DeleteAnnotationSetRequest) Reset()
func (x *DeleteAnnotationSetRequest) String() string
type DeleteCallSetRequest struct {
// The ID of the call set to be deleted.
CallSetId string `protobuf:"bytes,1,opt,name=call_set_id,json=callSetId,proto3" json:"call_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*DeleteCallSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use DeleteCallSetRequest.ProtoReflect.Descriptor instead.
func (x *DeleteCallSetRequest) GetCallSetId() string
func (*DeleteCallSetRequest) ProtoMessage()
func (x *DeleteCallSetRequest) ProtoReflect() protoreflect.Message
func (x *DeleteCallSetRequest) Reset()
func (x *DeleteCallSetRequest) String() string
type DeleteDatasetRequest struct {
// The ID of the dataset to be deleted.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// contains filtered or unexported fields
}
func (*DeleteDatasetRequest) Descriptor() ([]byte, []int)
Deprecated: Use DeleteDatasetRequest.ProtoReflect.Descriptor instead.
func (x *DeleteDatasetRequest) GetDatasetId() string
func (*DeleteDatasetRequest) ProtoMessage()
func (x *DeleteDatasetRequest) ProtoReflect() protoreflect.Message
func (x *DeleteDatasetRequest) Reset()
func (x *DeleteDatasetRequest) String() string
type DeleteReadGroupSetRequest struct {
// The ID of the read group set to be deleted. The caller must have WRITE
// permissions to the dataset associated with this read group set.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*DeleteReadGroupSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use DeleteReadGroupSetRequest.ProtoReflect.Descriptor instead.
func (x *DeleteReadGroupSetRequest) GetReadGroupSetId() string
func (*DeleteReadGroupSetRequest) ProtoMessage()
func (x *DeleteReadGroupSetRequest) ProtoReflect() protoreflect.Message
func (x *DeleteReadGroupSetRequest) Reset()
func (x *DeleteReadGroupSetRequest) String() string
type DeleteVariantRequest struct {
// The ID of the variant to be deleted.
VariantId string `protobuf:"bytes,1,opt,name=variant_id,json=variantId,proto3" json:"variant_id,omitempty"`
// contains filtered or unexported fields
}
func (*DeleteVariantRequest) Descriptor() ([]byte, []int)
Deprecated: Use DeleteVariantRequest.ProtoReflect.Descriptor instead.
func (x *DeleteVariantRequest) GetVariantId() string
func (*DeleteVariantRequest) ProtoMessage()
func (x *DeleteVariantRequest) ProtoReflect() protoreflect.Message
func (x *DeleteVariantRequest) Reset()
func (x *DeleteVariantRequest) String() string
The delete variant set request.
type DeleteVariantSetRequest struct {
// The ID of the variant set to be deleted.
VariantSetId string `protobuf:"bytes,1,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*DeleteVariantSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use DeleteVariantSetRequest.ProtoReflect.Descriptor instead.
func (x *DeleteVariantSetRequest) GetVariantSetId() string
func (*DeleteVariantSetRequest) ProtoMessage()
func (x *DeleteVariantSetRequest) ProtoReflect() protoreflect.Message
func (x *DeleteVariantSetRequest) Reset()
func (x *DeleteVariantSetRequest) String() string
The read group set export request.
type ExportReadGroupSetRequest struct {
// Required. The Google Cloud project ID that owns this
// export. The caller must have WRITE access to this project.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=export_uri,json=exportUri,proto3" json:"export_uri,omitempty"`
// Required. The ID of the read group set to export. The caller must have
// READ access to this read group set.
ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// 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 `protobuf:"bytes,4,rep,name=reference_names,json=referenceNames,proto3" json:"reference_names,omitempty"`
// contains filtered or unexported fields
}
func (*ExportReadGroupSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use ExportReadGroupSetRequest.ProtoReflect.Descriptor instead.
func (x *ExportReadGroupSetRequest) GetExportUri() string
func (x *ExportReadGroupSetRequest) GetProjectId() string
func (x *ExportReadGroupSetRequest) GetReadGroupSetId() string
func (x *ExportReadGroupSetRequest) GetReferenceNames() []string
func (*ExportReadGroupSetRequest) ProtoMessage()
func (x *ExportReadGroupSetRequest) ProtoReflect() protoreflect.Message
func (x *ExportReadGroupSetRequest) Reset()
func (x *ExportReadGroupSetRequest) String() string
The variant data export request.
type ExportVariantSetRequest struct {
// Required. The ID of the variant set that contains variant data which
// should be exported. The caller must have READ access to this variant set.
VariantSetId string `protobuf:"bytes,1,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// If provided, only variant call information from the specified call sets
// will be exported. By default all variant calls are exported.
CallSetIds []string `protobuf:"bytes,2,rep,name=call_set_ids,json=callSetIds,proto3" json:"call_set_ids,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// The format for the exported data.
Format ExportVariantSetRequest_Format `protobuf:"varint,4,opt,name=format,proto3,enum=google.genomics.v1.ExportVariantSetRequest_Format" json:"format,omitempty"`
// 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 `protobuf:"bytes,5,opt,name=bigquery_dataset,json=bigqueryDataset,proto3" json:"bigquery_dataset,omitempty"`
// 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 `protobuf:"bytes,6,opt,name=bigquery_table,json=bigqueryTable,proto3" json:"bigquery_table,omitempty"`
// contains filtered or unexported fields
}
func (*ExportVariantSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use ExportVariantSetRequest.ProtoReflect.Descriptor instead.
func (x *ExportVariantSetRequest) GetBigqueryDataset() string
func (x *ExportVariantSetRequest) GetBigqueryTable() string
func (x *ExportVariantSetRequest) GetCallSetIds() []string
func (x *ExportVariantSetRequest) GetFormat() ExportVariantSetRequest_Format
func (x *ExportVariantSetRequest) GetProjectId() string
func (x *ExportVariantSetRequest) GetVariantSetId() string
func (*ExportVariantSetRequest) ProtoMessage()
func (x *ExportVariantSetRequest) ProtoReflect() protoreflect.Message
func (x *ExportVariantSetRequest) Reset()
func (x *ExportVariantSetRequest) String() string
type ExportVariantSetRequest_Format int32
const (
ExportVariantSetRequest_FORMAT_UNSPECIFIED ExportVariantSetRequest_Format = 0
// Export the data to Google BigQuery.
ExportVariantSetRequest_FORMAT_BIGQUERY ExportVariantSetRequest_Format = 1
)
func (ExportVariantSetRequest_Format) Descriptor() protoreflect.EnumDescriptor
func (x ExportVariantSetRequest_Format) Enum() *ExportVariantSetRequest_Format
func (ExportVariantSetRequest_Format) EnumDescriptor() ([]byte, []int)
Deprecated: Use ExportVariantSetRequest_Format.Descriptor instead.
func (x ExportVariantSetRequest_Format) Number() protoreflect.EnumNumber
func (x ExportVariantSetRequest_Format) String() string
func (ExportVariantSetRequest_Format) Type() protoreflect.EnumType
type ExternalId struct {
// The name of the source of this data.
SourceName string `protobuf:"bytes,1,opt,name=source_name,json=sourceName,proto3" json:"source_name,omitempty"`
// The id used by the source of this data.
Id string `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
// contains filtered or unexported fields
}
func (*ExternalId) Descriptor() ([]byte, []int)
Deprecated: Use ExternalId.ProtoReflect.Descriptor instead.
func (x *ExternalId) GetId() string
func (x *ExternalId) GetSourceName() string
func (*ExternalId) ProtoMessage()
func (x *ExternalId) ProtoReflect() protoreflect.Message
func (x *ExternalId) Reset()
func (x *ExternalId) String() string
type GetAnnotationRequest struct {
// The ID of the annotation to be retrieved.
AnnotationId string `protobuf:"bytes,1,opt,name=annotation_id,json=annotationId,proto3" json:"annotation_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetAnnotationRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetAnnotationRequest.ProtoReflect.Descriptor instead.
func (x *GetAnnotationRequest) GetAnnotationId() string
func (*GetAnnotationRequest) ProtoMessage()
func (x *GetAnnotationRequest) ProtoReflect() protoreflect.Message
func (x *GetAnnotationRequest) Reset()
func (x *GetAnnotationRequest) String() string
type GetAnnotationSetRequest struct {
// The ID of the annotation set to be retrieved.
AnnotationSetId string `protobuf:"bytes,1,opt,name=annotation_set_id,json=annotationSetId,proto3" json:"annotation_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetAnnotationSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetAnnotationSetRequest.ProtoReflect.Descriptor instead.
func (x *GetAnnotationSetRequest) GetAnnotationSetId() string
func (*GetAnnotationSetRequest) ProtoMessage()
func (x *GetAnnotationSetRequest) ProtoReflect() protoreflect.Message
func (x *GetAnnotationSetRequest) Reset()
func (x *GetAnnotationSetRequest) String() string
type GetCallSetRequest struct {
// The ID of the call set.
CallSetId string `protobuf:"bytes,1,opt,name=call_set_id,json=callSetId,proto3" json:"call_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetCallSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetCallSetRequest.ProtoReflect.Descriptor instead.
func (x *GetCallSetRequest) GetCallSetId() string
func (*GetCallSetRequest) ProtoMessage()
func (x *GetCallSetRequest) ProtoReflect() protoreflect.Message
func (x *GetCallSetRequest) Reset()
func (x *GetCallSetRequest) String() string
type GetDatasetRequest struct {
// The ID of the dataset.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetDatasetRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetDatasetRequest.ProtoReflect.Descriptor instead.
func (x *GetDatasetRequest) GetDatasetId() string
func (*GetDatasetRequest) ProtoMessage()
func (x *GetDatasetRequest) ProtoReflect() protoreflect.Message
func (x *GetDatasetRequest) Reset()
func (x *GetDatasetRequest) String() string
type GetReadGroupSetRequest struct {
// The ID of the read group set.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetReadGroupSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetReadGroupSetRequest.ProtoReflect.Descriptor instead.
func (x *GetReadGroupSetRequest) GetReadGroupSetId() string
func (*GetReadGroupSetRequest) ProtoMessage()
func (x *GetReadGroupSetRequest) ProtoReflect() protoreflect.Message
func (x *GetReadGroupSetRequest) Reset()
func (x *GetReadGroupSetRequest) String() string
type GetReferenceRequest struct {
// The ID of the reference.
ReferenceId string `protobuf:"bytes,1,opt,name=reference_id,json=referenceId,proto3" json:"reference_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetReferenceRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetReferenceRequest.ProtoReflect.Descriptor instead.
func (x *GetReferenceRequest) GetReferenceId() string
func (*GetReferenceRequest) ProtoMessage()
func (x *GetReferenceRequest) ProtoReflect() protoreflect.Message
func (x *GetReferenceRequest) Reset()
func (x *GetReferenceRequest) String() string
type GetReferenceSetRequest struct {
// The ID of the reference set.
ReferenceSetId string `protobuf:"bytes,1,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetReferenceSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetReferenceSetRequest.ProtoReflect.Descriptor instead.
func (x *GetReferenceSetRequest) GetReferenceSetId() string
func (*GetReferenceSetRequest) ProtoMessage()
func (x *GetReferenceSetRequest) ProtoReflect() protoreflect.Message
func (x *GetReferenceSetRequest) Reset()
func (x *GetReferenceSetRequest) String() string
type GetVariantRequest struct {
// The ID of the variant.
VariantId string `protobuf:"bytes,1,opt,name=variant_id,json=variantId,proto3" json:"variant_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetVariantRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetVariantRequest.ProtoReflect.Descriptor instead.
func (x *GetVariantRequest) GetVariantId() string
func (*GetVariantRequest) ProtoMessage()
func (x *GetVariantRequest) ProtoReflect() protoreflect.Message
func (x *GetVariantRequest) Reset()
func (x *GetVariantRequest) String() string
The variant set request.
type GetVariantSetRequest struct {
// Required. The ID of the variant set.
VariantSetId string `protobuf:"bytes,1,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// contains filtered or unexported fields
}
func (*GetVariantSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use GetVariantSetRequest.ProtoReflect.Descriptor instead.
func (x *GetVariantSetRequest) GetVariantSetId() string
func (*GetVariantSetRequest) ProtoMessage()
func (x *GetVariantSetRequest) ProtoReflect() protoreflect.Message
func (x *GetVariantSetRequest) Reset()
func (x *GetVariantSetRequest) String() string
The read group set import request.
type ImportReadGroupSetsRequest struct {
// Required. The ID of the dataset these read group sets will belong to. The
// caller must have WRITE permissions to this dataset.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// 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 `protobuf:"bytes,2,rep,name=source_uris,json=sourceUris,proto3" json:"source_uris,omitempty"`
// The partition strategy describes how read groups are partitioned into read
// group sets.
PartitionStrategy ImportReadGroupSetsRequest_PartitionStrategy `protobuf:"varint,5,opt,name=partition_strategy,json=partitionStrategy,proto3,enum=google.genomics.v1.ImportReadGroupSetsRequest_PartitionStrategy" json:"partition_strategy,omitempty"`
// contains filtered or unexported fields
}
func (*ImportReadGroupSetsRequest) Descriptor() ([]byte, []int)
Deprecated: Use ImportReadGroupSetsRequest.ProtoReflect.Descriptor instead.
func (x *ImportReadGroupSetsRequest) GetDatasetId() string
func (x *ImportReadGroupSetsRequest) GetPartitionStrategy() ImportReadGroupSetsRequest_PartitionStrategy
func (x *ImportReadGroupSetsRequest) GetReferenceSetId() string
func (x *ImportReadGroupSetsRequest) GetSourceUris() []string
func (*ImportReadGroupSetsRequest) ProtoMessage()
func (x *ImportReadGroupSetsRequest) ProtoReflect() protoreflect.Message
func (x *ImportReadGroupSetsRequest) Reset()
func (x *ImportReadGroupSetsRequest) String() string
type ImportReadGroupSetsRequest_PartitionStrategy int32
const (
ImportReadGroupSetsRequest_PARTITION_STRATEGY_UNSPECIFIED ImportReadGroupSetsRequest_PartitionStrategy = 0
// 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.
ImportReadGroupSetsRequest_PER_FILE_PER_SAMPLE ImportReadGroupSetsRequest_PartitionStrategy = 1
// 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.
ImportReadGroupSetsRequest_MERGE_ALL ImportReadGroupSetsRequest_PartitionStrategy = 2
)
func (ImportReadGroupSetsRequest_PartitionStrategy) Descriptor() protoreflect.EnumDescriptor
func (x ImportReadGroupSetsRequest_PartitionStrategy) Enum() *ImportReadGroupSetsRequest_PartitionStrategy
func (ImportReadGroupSetsRequest_PartitionStrategy) EnumDescriptor() ([]byte, []int)
Deprecated: Use ImportReadGroupSetsRequest_PartitionStrategy.Descriptor instead.
func (x ImportReadGroupSetsRequest_PartitionStrategy) Number() protoreflect.EnumNumber
func (x ImportReadGroupSetsRequest_PartitionStrategy) String() string
func (ImportReadGroupSetsRequest_PartitionStrategy) Type() protoreflect.EnumType
The read group set import response.
type ImportReadGroupSetsResponse struct {
// IDs of the read group sets that were created.
ReadGroupSetIds []string `protobuf:"bytes,1,rep,name=read_group_set_ids,json=readGroupSetIds,proto3" json:"read_group_set_ids,omitempty"`
// contains filtered or unexported fields
}
func (*ImportReadGroupSetsResponse) Descriptor() ([]byte, []int)
Deprecated: Use ImportReadGroupSetsResponse.ProtoReflect.Descriptor instead.
func (x *ImportReadGroupSetsResponse) GetReadGroupSetIds() []string
func (*ImportReadGroupSetsResponse) ProtoMessage()
func (x *ImportReadGroupSetsResponse) ProtoReflect() protoreflect.Message
func (x *ImportReadGroupSetsResponse) Reset()
func (x *ImportReadGroupSetsResponse) String() string
The variant data import request.
type ImportVariantsRequest struct {
// Required. The variant set to which variant data should be imported.
VariantSetId string `protobuf:"bytes,1,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// 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 `protobuf:"bytes,2,rep,name=source_uris,json=sourceUris,proto3" json:"source_uris,omitempty"`
// The format of the variant data being imported. If unspecified, defaults to
// to `VCF`.
Format ImportVariantsRequest_Format `protobuf:"varint,3,opt,name=format,proto3,enum=google.genomics.v1.ImportVariantsRequest_Format" json:"format,omitempty"`
// 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 `protobuf:"varint,5,opt,name=normalize_reference_names,json=normalizeReferenceNames,proto3" json:"normalize_reference_names,omitempty"`
// 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]InfoMergeOperation `protobuf:"bytes,6,rep,name=info_merge_config,json=infoMergeConfig,proto3" json:"info_merge_config,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"varint,2,opt,name=value,proto3,enum=google.genomics.v1.InfoMergeOperation"`
// contains filtered or unexported fields
}
func (*ImportVariantsRequest) Descriptor() ([]byte, []int)
Deprecated: Use ImportVariantsRequest.ProtoReflect.Descriptor instead.
func (x *ImportVariantsRequest) GetFormat() ImportVariantsRequest_Format
func (x *ImportVariantsRequest) GetInfoMergeConfig() map[string]InfoMergeOperation
func (x *ImportVariantsRequest) GetNormalizeReferenceNames() bool
func (x *ImportVariantsRequest) GetSourceUris() []string
func (x *ImportVariantsRequest) GetVariantSetId() string
func (*ImportVariantsRequest) ProtoMessage()
func (x *ImportVariantsRequest) ProtoReflect() protoreflect.Message
func (x *ImportVariantsRequest) Reset()
func (x *ImportVariantsRequest) String() string
type ImportVariantsRequest_Format int32
const (
ImportVariantsRequest_FORMAT_UNSPECIFIED ImportVariantsRequest_Format = 0
// VCF (Variant Call Format). The VCF files may be gzip compressed. gVCF is
// also supported.
ImportVariantsRequest_FORMAT_VCF ImportVariantsRequest_Format = 1
// Complete Genomics masterVarBeta format. The masterVarBeta files may
// be bzip2 compressed.
ImportVariantsRequest_FORMAT_COMPLETE_GENOMICS ImportVariantsRequest_Format = 2
)
func (ImportVariantsRequest_Format) Descriptor() protoreflect.EnumDescriptor
func (x ImportVariantsRequest_Format) Enum() *ImportVariantsRequest_Format
func (ImportVariantsRequest_Format) EnumDescriptor() ([]byte, []int)
Deprecated: Use ImportVariantsRequest_Format.Descriptor instead.
func (x ImportVariantsRequest_Format) Number() protoreflect.EnumNumber
func (x ImportVariantsRequest_Format) String() string
func (ImportVariantsRequest_Format) Type() protoreflect.EnumType
The variant data import response.
type ImportVariantsResponse struct {
// IDs of the call sets created during the import.
CallSetIds []string `protobuf:"bytes,1,rep,name=call_set_ids,json=callSetIds,proto3" json:"call_set_ids,omitempty"`
// contains filtered or unexported fields
}
func (*ImportVariantsResponse) Descriptor() ([]byte, []int)
Deprecated: Use ImportVariantsResponse.ProtoReflect.Descriptor instead.
func (x *ImportVariantsResponse) GetCallSetIds() []string
func (*ImportVariantsResponse) ProtoMessage()
func (x *ImportVariantsResponse) ProtoReflect() protoreflect.Message
func (x *ImportVariantsResponse) Reset()
func (x *ImportVariantsResponse) String() string
Operations to be performed during import on Variant info fields. These operations are set for each info field in the info_merge_config map of ImportVariantsRequest, which is plumbed down to the MergeVariantRequests generated by the import job.
type InfoMergeOperation int32
const (
InfoMergeOperation_INFO_MERGE_OPERATION_UNSPECIFIED InfoMergeOperation = 0
// By default, Variant info fields are persisted if the Variant doesn't
// already exist in the variantset. If the Variant is equivalent to a
// Variant already in the variantset, the incoming Variant's info field
// is ignored in favor of that of the already persisted Variant.
InfoMergeOperation_IGNORE_NEW InfoMergeOperation = 1
// This operation removes an info field from the incoming Variant
// and persists this info field in each of the incoming Variant's Calls.
InfoMergeOperation_MOVE_TO_CALLS InfoMergeOperation = 2
)
func (InfoMergeOperation) Descriptor() protoreflect.EnumDescriptor
func (x InfoMergeOperation) Enum() *InfoMergeOperation
func (InfoMergeOperation) EnumDescriptor() ([]byte, []int)
Deprecated: Use InfoMergeOperation.Descriptor instead.
func (x InfoMergeOperation) Number() protoreflect.EnumNumber
func (x InfoMergeOperation) String() string
func (InfoMergeOperation) Type() protoreflect.EnumType
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 {
// The position of this alignment.
Position *Position `protobuf:"bytes,1,opt,name=position,proto3" json:"position,omitempty"`
// 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 int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality,proto3" json:"mapping_quality,omitempty"`
// Represents the local alignment of this sequence (alignment matches, indels,
// etc) against the reference.
Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar,proto3" json:"cigar,omitempty"`
// contains filtered or unexported fields
}
func (*LinearAlignment) Descriptor() ([]byte, []int)
Deprecated: Use LinearAlignment.ProtoReflect.Descriptor instead.
func (x *LinearAlignment) GetCigar() []*CigarUnit
func (x *LinearAlignment) GetMappingQuality() int32
func (x *LinearAlignment) GetPosition() *Position
func (*LinearAlignment) ProtoMessage()
func (x *LinearAlignment) ProtoReflect() protoreflect.Message
func (x *LinearAlignment) Reset()
func (x *LinearAlignment) String() string
type ListBasesRequest struct {
// The ID of the reference.
ReferenceId string `protobuf:"bytes,1,opt,name=reference_id,json=referenceId,proto3" json:"reference_id,omitempty"`
// The start position (0-based) of this query. Defaults to 0.
Start int64 `protobuf:"varint,2,opt,name=start,proto3" json:"start,omitempty"`
// The end position (0-based, exclusive) of this query. Defaults to the length
// of this reference.
End int64 `protobuf:"varint,3,opt,name=end,proto3" json:"end,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of bases to return in a single page. If unspecified,
// defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
// pairs).
PageSize int32 `protobuf:"varint,5,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*ListBasesRequest) Descriptor() ([]byte, []int)
Deprecated: Use ListBasesRequest.ProtoReflect.Descriptor instead.
func (x *ListBasesRequest) GetEnd() int64
func (x *ListBasesRequest) GetPageSize() int32
func (x *ListBasesRequest) GetPageToken() string
func (x *ListBasesRequest) GetReferenceId() string
func (x *ListBasesRequest) GetStart() int64
func (*ListBasesRequest) ProtoMessage()
func (x *ListBasesRequest) ProtoReflect() protoreflect.Message
func (x *ListBasesRequest) Reset()
func (x *ListBasesRequest) String() string
type ListBasesResponse struct {
// 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 `protobuf:"varint,1,opt,name=offset,proto3" json:"offset,omitempty"`
// A substring of the bases that make up this reference.
Sequence string `protobuf:"bytes,2,opt,name=sequence,proto3" json:"sequence,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*ListBasesResponse) Descriptor() ([]byte, []int)
Deprecated: Use ListBasesResponse.ProtoReflect.Descriptor instead.
func (x *ListBasesResponse) GetNextPageToken() string
func (x *ListBasesResponse) GetOffset() int64
func (x *ListBasesResponse) GetSequence() string
func (*ListBasesResponse) ProtoMessage()
func (x *ListBasesResponse) ProtoReflect() protoreflect.Message
func (x *ListBasesResponse) Reset()
func (x *ListBasesResponse) String() string
type ListCoverageBucketsRequest struct {
// Required. The ID of the read group set over which coverage is requested.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The name of the reference to query, within the reference set associated
// with this query. Optional.
ReferenceName string `protobuf:"bytes,3,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified. Defaults to 0.
Start int64 `protobuf:"varint,4,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified. If unset or 0, defaults
// to the length of the reference.
End int64 `protobuf:"varint,5,opt,name=end,proto3" json:"end,omitempty"`
// The desired width of each reported coverage bucket in base pairs. This
// will be rounded down to the nearest precomputed bucket width; the value
// of which is returned as `bucketWidth` in the response. Defaults
// to infinity (each bucket spans an entire reference sequence) or the length
// of the target range, if specified. The smallest precomputed
// `bucketWidth` is currently 2048 base pairs; this is subject to
// change.
TargetBucketWidth int64 `protobuf:"varint,6,opt,name=target_bucket_width,json=targetBucketWidth,proto3" json:"target_bucket_width,omitempty"`
// 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 `protobuf:"bytes,7,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 2048.
PageSize int32 `protobuf:"varint,8,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*ListCoverageBucketsRequest) Descriptor() ([]byte, []int)
Deprecated: Use ListCoverageBucketsRequest.ProtoReflect.Descriptor instead.
func (x *ListCoverageBucketsRequest) GetEnd() int64
func (x *ListCoverageBucketsRequest) GetPageSize() int32
func (x *ListCoverageBucketsRequest) GetPageToken() string
func (x *ListCoverageBucketsRequest) GetReadGroupSetId() string
func (x *ListCoverageBucketsRequest) GetReferenceName() string
func (x *ListCoverageBucketsRequest) GetStart() int64
func (x *ListCoverageBucketsRequest) GetTargetBucketWidth() int64
func (*ListCoverageBucketsRequest) ProtoMessage()
func (x *ListCoverageBucketsRequest) ProtoReflect() protoreflect.Message
func (x *ListCoverageBucketsRequest) Reset()
func (x *ListCoverageBucketsRequest) String() string
type ListCoverageBucketsResponse struct {
// 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 `protobuf:"varint,1,opt,name=bucket_width,json=bucketWidth,proto3" json:"bucket_width,omitempty"`
// 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 `protobuf:"bytes,2,rep,name=coverage_buckets,json=coverageBuckets,proto3" json:"coverage_buckets,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*ListCoverageBucketsResponse) Descriptor() ([]byte, []int)
Deprecated: Use ListCoverageBucketsResponse.ProtoReflect.Descriptor instead.
func (x *ListCoverageBucketsResponse) GetBucketWidth() int64
func (x *ListCoverageBucketsResponse) GetCoverageBuckets() []*CoverageBucket
func (x *ListCoverageBucketsResponse) GetNextPageToken() string
func (*ListCoverageBucketsResponse) ProtoMessage()
func (x *ListCoverageBucketsResponse) ProtoReflect() protoreflect.Message
func (x *ListCoverageBucketsResponse) Reset()
func (x *ListCoverageBucketsResponse) String() string
The dataset list request.
type ListDatasetsRequest struct {
// Required. The Google Cloud project ID to list datasets for.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 50. The maximum value is 1024.
PageSize int32 `protobuf:"varint,2,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// contains filtered or unexported fields
}
func (*ListDatasetsRequest) Descriptor() ([]byte, []int)
Deprecated: Use ListDatasetsRequest.ProtoReflect.Descriptor instead.
func (x *ListDatasetsRequest) GetPageSize() int32
func (x *ListDatasetsRequest) GetPageToken() string
func (x *ListDatasetsRequest) GetProjectId() string
func (*ListDatasetsRequest) ProtoMessage()
func (x *ListDatasetsRequest) ProtoReflect() protoreflect.Message
func (x *ListDatasetsRequest) Reset()
func (x *ListDatasetsRequest) String() string
The dataset list response.
type ListDatasetsResponse struct {
// The list of matching Datasets.
Datasets []*Dataset `protobuf:"bytes,1,rep,name=datasets,proto3" json:"datasets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*ListDatasetsResponse) Descriptor() ([]byte, []int)
Deprecated: Use ListDatasetsResponse.ProtoReflect.Descriptor instead.
func (x *ListDatasetsResponse) GetDatasets() []*Dataset
func (x *ListDatasetsResponse) GetNextPageToken() string
func (*ListDatasetsResponse) ProtoMessage()
func (x *ListDatasetsResponse) ProtoReflect() protoreflect.Message
func (x *ListDatasetsResponse) Reset()
func (x *ListDatasetsResponse) String() string
type MergeVariantsRequest struct {
// The destination variant set.
VariantSetId string `protobuf:"bytes,1,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// The variants to be merged with existing variants.
Variants []*Variant `protobuf:"bytes,2,rep,name=variants,proto3" json:"variants,omitempty"`
// A mapping between info field keys and the InfoMergeOperations to
// be performed on them.
InfoMergeConfig map[string]InfoMergeOperation `protobuf:"bytes,3,rep,name=info_merge_config,json=infoMergeConfig,proto3" json:"info_merge_config,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"varint,2,opt,name=value,proto3,enum=google.genomics.v1.InfoMergeOperation"`
// contains filtered or unexported fields
}
func (*MergeVariantsRequest) Descriptor() ([]byte, []int)
Deprecated: Use MergeVariantsRequest.ProtoReflect.Descriptor instead.
func (x *MergeVariantsRequest) GetInfoMergeConfig() map[string]InfoMergeOperation
func (x *MergeVariantsRequest) GetVariantSetId() string
func (x *MergeVariantsRequest) GetVariants() []*Variant
func (*MergeVariantsRequest) ProtoMessage()
func (x *MergeVariantsRequest) ProtoReflect() protoreflect.Message
func (x *MergeVariantsRequest) Reset()
func (x *MergeVariantsRequest) String() string
An event that occurred during an [Operation][google.longrunning.Operation].
type OperationEvent struct {
// Optional time of when event started.
StartTime *timestamppb.Timestamp `protobuf:"bytes,1,opt,name=start_time,json=startTime,proto3" json:"start_time,omitempty"`
// 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 *timestamppb.Timestamp `protobuf:"bytes,2,opt,name=end_time,json=endTime,proto3" json:"end_time,omitempty"`
// Required description of event.
Description string `protobuf:"bytes,3,opt,name=description,proto3" json:"description,omitempty"`
// contains filtered or unexported fields
}
func (*OperationEvent) Descriptor() ([]byte, []int)
Deprecated: Use OperationEvent.ProtoReflect.Descriptor instead.
func (x *OperationEvent) GetDescription() string
func (x *OperationEvent) GetEndTime() *timestamppb.Timestamp
func (x *OperationEvent) GetStartTime() *timestamppb.Timestamp
func (*OperationEvent) ProtoMessage()
func (x *OperationEvent) ProtoReflect() protoreflect.Message
func (x *OperationEvent) Reset()
func (x *OperationEvent) String() string
Metadata describing an [Operation][google.longrunning.Operation].
type OperationMetadata struct {
// The Google Cloud Project in which the job is scoped.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// The time at which the job was submitted to the Genomics service.
CreateTime *timestamppb.Timestamp `protobuf:"bytes,2,opt,name=create_time,json=createTime,proto3" json:"create_time,omitempty"`
// The time at which the job began to run.
StartTime *timestamppb.Timestamp `protobuf:"bytes,3,opt,name=start_time,json=startTime,proto3" json:"start_time,omitempty"`
// The time at which the job stopped running.
EndTime *timestamppb.Timestamp `protobuf:"bytes,4,opt,name=end_time,json=endTime,proto3" json:"end_time,omitempty"`
// 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 *anypb.Any `protobuf:"bytes,5,opt,name=request,proto3" json:"request,omitempty"`
// 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 `protobuf:"bytes,6,rep,name=events,proto3" json:"events,omitempty"`
// This field is deprecated. Use `labels` instead. Optionally provided by the
// caller when submitting the request that creates the operation.
ClientId string `protobuf:"bytes,7,opt,name=client_id,json=clientId,proto3" json:"client_id,omitempty"`
// Runtime metadata on this Operation.
RuntimeMetadata *anypb.Any `protobuf:"bytes,8,opt,name=runtime_metadata,json=runtimeMetadata,proto3" json:"runtime_metadata,omitempty"`
// Optionally provided by the caller when submitting the request that creates
// the operation.
Labels map[string]string `protobuf:"bytes,9,rep,name=labels,proto3" json:"labels,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*OperationMetadata) Descriptor() ([]byte, []int)
Deprecated: Use OperationMetadata.ProtoReflect.Descriptor instead.
func (x *OperationMetadata) GetClientId() string
func (x *OperationMetadata) GetCreateTime() *timestamppb.Timestamp
func (x *OperationMetadata) GetEndTime() *timestamppb.Timestamp
func (x *OperationMetadata) GetEvents() []*OperationEvent
func (x *OperationMetadata) GetLabels() map[string]string
func (x *OperationMetadata) GetProjectId() string
func (x *OperationMetadata) GetRequest() *anypb.Any
func (x *OperationMetadata) GetRuntimeMetadata() *anypb.Any
func (x *OperationMetadata) GetStartTime() *timestamppb.Timestamp
func (*OperationMetadata) ProtoMessage()
func (x *OperationMetadata) ProtoReflect() protoreflect.Message
func (x *OperationMetadata) Reset()
func (x *OperationMetadata) String() string
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 {
// The name of the reference in whatever reference set is being used.
ReferenceName string `protobuf:"bytes,1,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The 0-based offset from the start of the forward strand for that reference.
Position int64 `protobuf:"varint,2,opt,name=position,proto3" json:"position,omitempty"`
// Whether this position is on the reverse strand, as opposed to the forward
// strand.
ReverseStrand bool `protobuf:"varint,3,opt,name=reverse_strand,json=reverseStrand,proto3" json:"reverse_strand,omitempty"`
// contains filtered or unexported fields
}
func (*Position) Descriptor() ([]byte, []int)
Deprecated: Use Position.ProtoReflect.Descriptor instead.
func (x *Position) GetPosition() int64
func (x *Position) GetReferenceName() string
func (x *Position) GetReverseStrand() bool
func (*Position) ProtoMessage()
func (x *Position) ProtoReflect() protoreflect.Message
func (x *Position) Reset()
func (x *Position) String() string
A 0-based half-open genomic coordinate range for search requests.
type Range struct {
// The reference sequence name, for example `chr1`,
// `1`, or `chrX`.
ReferenceName string `protobuf:"bytes,1,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive.
Start int64 `protobuf:"varint,2,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive.
End int64 `protobuf:"varint,3,opt,name=end,proto3" json:"end,omitempty"`
// contains filtered or unexported fields
}
func (*Range) Descriptor() ([]byte, []int)
Deprecated: Use Range.ProtoReflect.Descriptor instead.
func (x *Range) GetEnd() int64
func (x *Range) GetReferenceName() string
func (x *Range) GetStart() int64
func (*Range) ProtoMessage()
func (x *Range) ProtoReflect() protoreflect.Message
func (x *Range) Reset()
func (x *Range) String() string
A read alignment describes a linear alignment of a string of DNA to a [reference sequence][google.genomics.v1.Reference], in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one [read group set][google.genomics.v1.ReadGroupSet].
For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-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 {
// The server-generated read ID, unique across all reads. This is different
// from the `fragmentName`.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// 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][google.genomics.v1.ReadGroup.name]).
ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId,proto3" json:"read_group_id,omitempty"`
// The ID of the read group set this read belongs to. A read belongs to
// exactly one read group set.
ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The fragment name. Equivalent to QNAME (query template name) in SAM.
FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName,proto3" json:"fragment_name,omitempty"`
// The orientation and the distance between reads from the fragment are
// consistent with the sequencing protocol (SAM flag 0x2).
ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement,proto3" json:"proper_placement,omitempty"`
// The fragment is a PCR or optical duplicate (SAM flag 0x400).
DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment,proto3" json:"duplicate_fragment,omitempty"`
// The observed length of the fragment, equivalent to TLEN in SAM.
FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength,proto3" json:"fragment_length,omitempty"`
// The read number in sequencing. 0-based and less than numberReads. This
// field replaces SAM flag 0x40 and 0x80.
ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber,proto3" json:"read_number,omitempty"`
// The number of reads in the fragment (extension to SAM flag 0x1).
NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads,proto3" json:"number_reads,omitempty"`
// Whether this read did not pass filters, such as platform or vendor quality
// controls (SAM flag 0x200).
FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks,proto3" json:"failed_vendor_quality_checks,omitempty"`
// The linear alignment for this alignment record. This field is null for
// unmapped reads.
Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment,proto3" json:"alignment,omitempty"`
// 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 `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment,proto3" json:"secondary_alignment,omitempty"`
// 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 `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment,proto3" json:"supplementary_alignment,omitempty"`
// 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 `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence,proto3" json:"aligned_sequence,omitempty"`
// 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 []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality,proto3" json:"aligned_quality,omitempty"`
// 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 `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition,proto3" json:"next_mate_position,omitempty"`
// 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]*structpb.ListValue `protobuf:"bytes,17,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*Read) Descriptor() ([]byte, []int)
Deprecated: Use Read.ProtoReflect.Descriptor instead.
func (x *Read) GetAlignedQuality() []int32
func (x *Read) GetAlignedSequence() string
func (x *Read) GetAlignment() *LinearAlignment
func (x *Read) GetDuplicateFragment() bool
func (x *Read) GetFailedVendorQualityChecks() bool
func (x *Read) GetFragmentLength() int32
func (x *Read) GetFragmentName() string
func (x *Read) GetId() string
func (x *Read) GetInfo() map[string]*structpb.ListValue
func (x *Read) GetNextMatePosition() *Position
func (x *Read) GetNumberReads() int32
func (x *Read) GetProperPlacement() bool
func (x *Read) GetReadGroupId() string
func (x *Read) GetReadGroupSetId() string
func (x *Read) GetReadNumber() int32
func (x *Read) GetSecondaryAlignment() bool
func (x *Read) GetSupplementaryAlignment() bool
func (*Read) ProtoMessage()
func (x *Read) ProtoReflect() protoreflect.Message
func (x *Read) Reset()
func (x *Read) String() string
A read group is all the data that's processed the same way by the sequencer.
type ReadGroup struct {
// 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][google.genomics.v1.ReadGroup.name].
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The dataset to which this read group belongs.
DatasetId string `protobuf:"bytes,2,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// The read group name. This corresponds to the @RG ID field in the SAM spec.
Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,omitempty"`
// A free-form text description of this read group.
Description string `protobuf:"bytes,4,opt,name=description,proto3" json:"description,omitempty"`
// A client-supplied sample identifier for the reads in this read group.
SampleId string `protobuf:"bytes,5,opt,name=sample_id,json=sampleId,proto3" json:"sample_id,omitempty"`
// The experiment used to generate this read group.
Experiment *ReadGroup_Experiment `protobuf:"bytes,6,opt,name=experiment,proto3" json:"experiment,omitempty"`
// 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 int32 `protobuf:"varint,7,opt,name=predicted_insert_size,json=predictedInsertSize,proto3" json:"predicted_insert_size,omitempty"`
// 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 []*ReadGroup_Program `protobuf:"bytes,10,rep,name=programs,proto3" json:"programs,omitempty"`
// The reference set the reads in this read group are aligned to.
ReferenceSetId string `protobuf:"bytes,11,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// 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]*structpb.ListValue `protobuf:"bytes,12,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*ReadGroup) Descriptor() ([]byte, []int)
Deprecated: Use ReadGroup.ProtoReflect.Descriptor instead.
func (x *ReadGroup) GetDatasetId() string
func (x *ReadGroup) GetDescription() string
func (x *ReadGroup) GetExperiment() *ReadGroup_Experiment
func (x *ReadGroup) GetId() string
func (x *ReadGroup) GetInfo() map[string]*structpb.ListValue
func (x *ReadGroup) GetName() string
func (x *ReadGroup) GetPredictedInsertSize() int32
func (x *ReadGroup) GetPrograms() []*ReadGroup_Program
func (x *ReadGroup) GetReferenceSetId() string
func (x *ReadGroup) GetSampleId() string
func (*ReadGroup) ProtoMessage()
func (x *ReadGroup) ProtoReflect() protoreflect.Message
func (x *ReadGroup) Reset()
func (x *ReadGroup) String() string
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-google-genomics)
type ReadGroupSet struct {
// The server-generated read group set ID, unique for all read group sets.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The dataset to which this read group set belongs.
DatasetId string `protobuf:"bytes,2,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// The reference set to which the reads in this read group set are aligned.
ReferenceSetId string `protobuf:"bytes,3,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=name,proto3" json:"name,omitempty"`
// The filename of the original source file for this read group set, if any.
Filename string `protobuf:"bytes,5,opt,name=filename,proto3" json:"filename,omitempty"`
// The read groups in this set. There are typically 1-10 read groups in a read
// group set.
ReadGroups []*ReadGroup `protobuf:"bytes,6,rep,name=read_groups,json=readGroups,proto3" json:"read_groups,omitempty"`
// A map of additional read group set information.
Info map[string]*structpb.ListValue `protobuf:"bytes,7,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*ReadGroupSet) Descriptor() ([]byte, []int)
Deprecated: Use ReadGroupSet.ProtoReflect.Descriptor instead.
func (x *ReadGroupSet) GetDatasetId() string
func (x *ReadGroupSet) GetFilename() string
func (x *ReadGroupSet) GetId() string
func (x *ReadGroupSet) GetInfo() map[string]*structpb.ListValue
func (x *ReadGroupSet) GetName() string
func (x *ReadGroupSet) GetReadGroups() []*ReadGroup
func (x *ReadGroupSet) GetReferenceSetId() string
func (*ReadGroupSet) ProtoMessage()
func (x *ReadGroupSet) ProtoReflect() protoreflect.Message
func (x *ReadGroupSet) Reset()
func (x *ReadGroupSet) String() string
type ReadGroup_Experiment struct {
// 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 `protobuf:"bytes,1,opt,name=library_id,json=libraryId,proto3" json:"library_id,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=platform_unit,json=platformUnit,proto3" json:"platform_unit,omitempty"`
// The sequencing center used as part of this experiment.
SequencingCenter string `protobuf:"bytes,3,opt,name=sequencing_center,json=sequencingCenter,proto3" json:"sequencing_center,omitempty"`
// The instrument model used as part of this experiment. This maps to
// sequencing technology in the SAM spec.
InstrumentModel string `protobuf:"bytes,4,opt,name=instrument_model,json=instrumentModel,proto3" json:"instrument_model,omitempty"`
// contains filtered or unexported fields
}
func (*ReadGroup_Experiment) Descriptor() ([]byte, []int)
Deprecated: Use ReadGroup_Experiment.ProtoReflect.Descriptor instead.
func (x *ReadGroup_Experiment) GetInstrumentModel() string
func (x *ReadGroup_Experiment) GetLibraryId() string
func (x *ReadGroup_Experiment) GetPlatformUnit() string
func (x *ReadGroup_Experiment) GetSequencingCenter() string
func (*ReadGroup_Experiment) ProtoMessage()
func (x *ReadGroup_Experiment) ProtoReflect() protoreflect.Message
func (x *ReadGroup_Experiment) Reset()
func (x *ReadGroup_Experiment) String() string
type ReadGroup_Program struct {
// The command line used to run this program.
CommandLine string `protobuf:"bytes,1,opt,name=command_line,json=commandLine,proto3" json:"command_line,omitempty"`
// The user specified locally unique ID of the program. Used along with
// `prevProgramId` to define an ordering between programs.
Id string `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
// The display name of the program. This is typically the colloquial name of
// the tool used, for example 'bwa' or 'picard'.
Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,omitempty"`
// The ID of the program run before this one.
PrevProgramId string `protobuf:"bytes,4,opt,name=prev_program_id,json=prevProgramId,proto3" json:"prev_program_id,omitempty"`
// The version of the program run.
Version string `protobuf:"bytes,5,opt,name=version,proto3" json:"version,omitempty"`
// contains filtered or unexported fields
}
func (*ReadGroup_Program) Descriptor() ([]byte, []int)
Deprecated: Use ReadGroup_Program.ProtoReflect.Descriptor instead.
func (x *ReadGroup_Program) GetCommandLine() string
func (x *ReadGroup_Program) GetId() string
func (x *ReadGroup_Program) GetName() string
func (x *ReadGroup_Program) GetPrevProgramId() string
func (x *ReadGroup_Program) GetVersion() string
func (*ReadGroup_Program) ProtoMessage()
func (x *ReadGroup_Program) ProtoReflect() protoreflect.Message
func (x *ReadGroup_Program) Reset()
func (x *ReadGroup_Program) String() string
ReadServiceV1Client is the client API for ReadServiceV1 service.
For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.
type ReadServiceV1Client interface {
// Creates read group sets by asynchronously importing the provided
// information.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// The caller must have WRITE permissions to the dataset.
//
// ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
//
// - Tags will be converted to strings - tag types are not preserved
// - Comments (`@CO`) in the input file header will not be preserved
// - Original header order of references (`@SQ`) will not be preserved
// - Any reverse stranded unmapped reads will be reverse complemented, and
// their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
// - Unmapped reads will be stripped of positional information (reference name
// and position)
ImportReadGroupSets(ctx context.Context, in *ImportReadGroupSetsRequest, opts ...grpc.CallOption) (*longrunningpb.Operation, error)
// Exports a read group set to a BAM file in Google Cloud Storage.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Note that currently there may be some differences between exported BAM
// files and the original BAM file at the time of import. See
// [ImportReadGroupSets][google.genomics.v1.ReadServiceV1.ImportReadGroupSets]
// for caveats.
ExportReadGroupSet(ctx context.Context, in *ExportReadGroupSetRequest, opts ...grpc.CallOption) (*longrunningpb.Operation, error)
// Searches for read group sets matching the criteria.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
SearchReadGroupSets(ctx context.Context, in *SearchReadGroupSetsRequest, opts ...grpc.CallOption) (*SearchReadGroupSetsResponse, error)
// Updates a read group set.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateReadGroupSet(ctx context.Context, in *UpdateReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error)
// Deletes a read group set.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteReadGroupSet(ctx context.Context, in *DeleteReadGroupSetRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// Gets a read group set by ID.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetReadGroupSet(ctx context.Context, in *GetReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error)
// Lists fixed width coverage buckets for a read group set, each of which
// correspond to a range of a reference sequence. Each bucket summarizes
// coverage information across its corresponding genomic range.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Coverage is defined as the number of reads which are aligned to a given
// base in the reference sequence. Coverage buckets are available at several
// precomputed bucket widths, enabling retrieval of various coverage 'zoom
// levels'. The caller must have READ permissions for the target read group
// set.
ListCoverageBuckets(ctx context.Context, in *ListCoverageBucketsRequest, opts ...grpc.CallOption) (*ListCoverageBucketsResponse, error)
// Gets a list of reads for one or more read group sets.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Reads search operates over a genomic coordinate space of reference sequence
// & position defined over the reference sequences to which the requested
// read group sets are aligned.
//
// If a target positional range is specified, search returns all reads whose
// alignment to the reference genome overlap the range. A query which
// specifies only read group set IDs yields all reads in those read group
// sets, including unmapped reads.
//
// All reads returned (including reads on subsequent pages) are ordered by
// genomic coordinate (by reference sequence, then position). Reads with
// equivalent genomic coordinates are returned in an unspecified order. This
// order is consistent, such that two queries for the same content (regardless
// of page size) yield reads in the same order across their respective streams
// of paginated responses.
//
// Implements
// [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
SearchReads(ctx context.Context, in *SearchReadsRequest, opts ...grpc.CallOption) (*SearchReadsResponse, error)
}
func NewReadServiceV1Client(cc grpc.ClientConnInterface) ReadServiceV1Client
ReadServiceV1Server is the server API for ReadServiceV1 service.
type ReadServiceV1Server interface {
// Creates read group sets by asynchronously importing the provided
// information.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// The caller must have WRITE permissions to the dataset.
//
// ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
//
// - Tags will be converted to strings - tag types are not preserved
// - Comments (`@CO`) in the input file header will not be preserved
// - Original header order of references (`@SQ`) will not be preserved
// - Any reverse stranded unmapped reads will be reverse complemented, and
// their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
// - Unmapped reads will be stripped of positional information (reference name
// and position)
ImportReadGroupSets(context.Context, *ImportReadGroupSetsRequest) (*longrunningpb.Operation, error)
// Exports a read group set to a BAM file in Google Cloud Storage.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Note that currently there may be some differences between exported BAM
// files and the original BAM file at the time of import. See
// [ImportReadGroupSets][google.genomics.v1.ReadServiceV1.ImportReadGroupSets]
// for caveats.
ExportReadGroupSet(context.Context, *ExportReadGroupSetRequest) (*longrunningpb.Operation, error)
// Searches for read group sets matching the criteria.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
SearchReadGroupSets(context.Context, *SearchReadGroupSetsRequest) (*SearchReadGroupSetsResponse, error)
// Updates a read group set.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateReadGroupSet(context.Context, *UpdateReadGroupSetRequest) (*ReadGroupSet, error)
// Deletes a read group set.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteReadGroupSet(context.Context, *DeleteReadGroupSetRequest) (*emptypb.Empty, error)
// Gets a read group set by ID.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetReadGroupSet(context.Context, *GetReadGroupSetRequest) (*ReadGroupSet, error)
// Lists fixed width coverage buckets for a read group set, each of which
// correspond to a range of a reference sequence. Each bucket summarizes
// coverage information across its corresponding genomic range.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Coverage is defined as the number of reads which are aligned to a given
// base in the reference sequence. Coverage buckets are available at several
// precomputed bucket widths, enabling retrieval of various coverage 'zoom
// levels'. The caller must have READ permissions for the target read group
// set.
ListCoverageBuckets(context.Context, *ListCoverageBucketsRequest) (*ListCoverageBucketsResponse, error)
// Gets a list of reads for one or more read group sets.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Reads search operates over a genomic coordinate space of reference sequence
// & position defined over the reference sequences to which the requested
// read group sets are aligned.
//
// If a target positional range is specified, search returns all reads whose
// alignment to the reference genome overlap the range. A query which
// specifies only read group set IDs yields all reads in those read group
// sets, including unmapped reads.
//
// All reads returned (including reads on subsequent pages) are ordered by
// genomic coordinate (by reference sequence, then position). Reads with
// equivalent genomic coordinates are returned in an unspecified order. This
// order is consistent, such that two queries for the same content (regardless
// of page size) yield reads in the same order across their respective streams
// of paginated responses.
//
// Implements
// [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
SearchReads(context.Context, *SearchReadsRequest) (*SearchReadsResponse, error)
}
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-google-genomics)
type Reference struct {
// The server-generated reference ID, unique across all references.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The length of this reference's sequence.
Length int64 `protobuf:"varint,2,opt,name=length,proto3" json:"length,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=md5checksum,proto3" json:"md5checksum,omitempty"`
// The name of this reference, for example `22`.
Name string `protobuf:"bytes,4,opt,name=name,proto3" json:"name,omitempty"`
// The URI from which the sequence was obtained. Typically specifies a FASTA
// format file.
SourceUri string `protobuf:"bytes,5,opt,name=source_uri,json=sourceUri,proto3" json:"source_uri,omitempty"`
// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
// with a version number, for example `GCF_000001405.26`.
SourceAccessions []string `protobuf:"bytes,6,rep,name=source_accessions,json=sourceAccessions,proto3" json:"source_accessions,omitempty"`
// ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
NcbiTaxonId int32 `protobuf:"varint,7,opt,name=ncbi_taxon_id,json=ncbiTaxonId,proto3" json:"ncbi_taxon_id,omitempty"`
// contains filtered or unexported fields
}
func (*Reference) Descriptor() ([]byte, []int)
Deprecated: Use Reference.ProtoReflect.Descriptor instead.
func (x *Reference) GetId() string
func (x *Reference) GetLength() int64
func (x *Reference) GetMd5Checksum() string
func (x *Reference) GetName() string
func (x *Reference) GetNcbiTaxonId() int32
func (x *Reference) GetSourceAccessions() []string
func (x *Reference) GetSourceUri() string
func (*Reference) ProtoMessage()
func (x *Reference) ProtoReflect() protoreflect.Message
func (x *Reference) Reset()
func (x *Reference) String() string
ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
type ReferenceBound struct {
// The name of the reference associated with this reference bound.
ReferenceName string `protobuf:"bytes,1,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// An upper bound (inclusive) on the starting coordinate of any
// variant in the reference sequence.
UpperBound int64 `protobuf:"varint,2,opt,name=upper_bound,json=upperBound,proto3" json:"upper_bound,omitempty"`
// contains filtered or unexported fields
}
func (*ReferenceBound) Descriptor() ([]byte, []int)
Deprecated: Use ReferenceBound.ProtoReflect.Descriptor instead.
func (x *ReferenceBound) GetReferenceName() string
func (x *ReferenceBound) GetUpperBound() int64
func (*ReferenceBound) ProtoMessage()
func (x *ReferenceBound) ProtoReflect() protoreflect.Message
func (x *ReferenceBound) Reset()
func (x *ReferenceBound) String() string
ReferenceServiceV1Client is the client API for ReferenceServiceV1 service.
For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.
type ReferenceServiceV1Client interface {
// Searches for reference sets which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
SearchReferenceSets(ctx context.Context, in *SearchReferenceSetsRequest, opts ...grpc.CallOption) (*SearchReferenceSetsResponse, error)
// Gets a reference set.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
GetReferenceSet(ctx context.Context, in *GetReferenceSetRequest, opts ...grpc.CallOption) (*ReferenceSet, error)
// Searches for references which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
SearchReferences(ctx context.Context, in *SearchReferencesRequest, opts ...grpc.CallOption) (*SearchReferencesResponse, error)
// Gets a reference.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
GetReference(ctx context.Context, in *GetReferenceRequest, opts ...grpc.CallOption) (*Reference, error)
// Lists the bases in a reference, optionally restricted to a range.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
ListBases(ctx context.Context, in *ListBasesRequest, opts ...grpc.CallOption) (*ListBasesResponse, error)
}
func NewReferenceServiceV1Client(cc grpc.ClientConnInterface) ReferenceServiceV1Client
ReferenceServiceV1Server is the server API for ReferenceServiceV1 service.
type ReferenceServiceV1Server interface {
// Searches for reference sets which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
SearchReferenceSets(context.Context, *SearchReferenceSetsRequest) (*SearchReferenceSetsResponse, error)
// Gets a reference set.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
GetReferenceSet(context.Context, *GetReferenceSetRequest) (*ReferenceSet, error)
// Searches for references which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
SearchReferences(context.Context, *SearchReferencesRequest) (*SearchReferencesResponse, error)
// Gets a reference.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
GetReference(context.Context, *GetReferenceRequest) (*Reference, error)
// Lists the bases in a reference, optionally restricted to a range.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
ListBases(context.Context, *ListBasesRequest) (*ListBasesResponse, error)
}
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-google-genomics)
type ReferenceSet struct {
// The server-generated reference set ID, unique across all reference sets.
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
// The IDs of the reference objects that are part of this set.
// `Reference.md5checksum` must be unique within this set.
ReferenceIds []string `protobuf:"bytes,2,rep,name=reference_ids,json=referenceIds,proto3" json:"reference_ids,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=md5checksum,proto3" json:"md5checksum,omitempty"`
// 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 int32 `protobuf:"varint,4,opt,name=ncbi_taxon_id,json=ncbiTaxonId,proto3" json:"ncbi_taxon_id,omitempty"`
// Free text description of this reference set.
Description string `protobuf:"bytes,5,opt,name=description,proto3" json:"description,omitempty"`
// Public id of this reference set, such as `GRCh37`.
AssemblyId string `protobuf:"bytes,6,opt,name=assembly_id,json=assemblyId,proto3" json:"assembly_id,omitempty"`
// The URI from which the references were obtained.
SourceUri string `protobuf:"bytes,7,opt,name=source_uri,json=sourceUri,proto3" json:"source_uri,omitempty"`
// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
// with a version number, for example `NC_000001.11`.
SourceAccessions []string `protobuf:"bytes,8,rep,name=source_accessions,json=sourceAccessions,proto3" json:"source_accessions,omitempty"`
// contains filtered or unexported fields
}
func (*ReferenceSet) Descriptor() ([]byte, []int)
Deprecated: Use ReferenceSet.ProtoReflect.Descriptor instead.
func (x *ReferenceSet) GetAssemblyId() string
func (x *ReferenceSet) GetDescription() string
func (x *ReferenceSet) GetId() string
func (x *ReferenceSet) GetMd5Checksum() string
func (x *ReferenceSet) GetNcbiTaxonId() int32
func (x *ReferenceSet) GetReferenceIds() []string
func (x *ReferenceSet) GetSourceAccessions() []string
func (x *ReferenceSet) GetSourceUri() string
func (*ReferenceSet) ProtoMessage()
func (x *ReferenceSet) ProtoReflect() protoreflect.Message
func (x *ReferenceSet) Reset()
func (x *ReferenceSet) String() string
type SearchAnnotationSetsRequest struct {
// Required. The dataset IDs to search within. Caller must have `READ` access
// to these datasets.
DatasetIds []string `protobuf:"bytes,1,rep,name=dataset_ids,json=datasetIds,proto3" json:"dataset_ids,omitempty"`
// If specified, only annotation sets associated with the given reference set
// are returned.
ReferenceSetId string `protobuf:"bytes,2,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// Only return annotations sets for which a substring of the name matches this
// string (case insensitive).
Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,omitempty"`
// If specified, only annotation sets that have any of these types are
// returned.
Types []AnnotationType `protobuf:"varint,4,rep,packed,name=types,proto3,enum=google.genomics.v1.AnnotationType" json:"types,omitempty"`
// 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 `protobuf:"bytes,5,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 128. The maximum value is 1024.
PageSize int32 `protobuf:"varint,6,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchAnnotationSetsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchAnnotationSetsRequest.ProtoReflect.Descriptor instead.
func (x *SearchAnnotationSetsRequest) GetDatasetIds() []string
func (x *SearchAnnotationSetsRequest) GetName() string
func (x *SearchAnnotationSetsRequest) GetPageSize() int32
func (x *SearchAnnotationSetsRequest) GetPageToken() string
func (x *SearchAnnotationSetsRequest) GetReferenceSetId() string
func (x *SearchAnnotationSetsRequest) GetTypes() []AnnotationType
func (*SearchAnnotationSetsRequest) ProtoMessage()
func (x *SearchAnnotationSetsRequest) ProtoReflect() protoreflect.Message
func (x *SearchAnnotationSetsRequest) Reset()
func (x *SearchAnnotationSetsRequest) String() string
type SearchAnnotationSetsResponse struct {
// The matching annotation sets.
AnnotationSets []*AnnotationSet `protobuf:"bytes,1,rep,name=annotation_sets,json=annotationSets,proto3" json:"annotation_sets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchAnnotationSetsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchAnnotationSetsResponse.ProtoReflect.Descriptor instead.
func (x *SearchAnnotationSetsResponse) GetAnnotationSets() []*AnnotationSet
func (x *SearchAnnotationSetsResponse) GetNextPageToken() string
func (*SearchAnnotationSetsResponse) ProtoMessage()
func (x *SearchAnnotationSetsResponse) ProtoReflect() protoreflect.Message
func (x *SearchAnnotationSetsResponse) Reset()
func (x *SearchAnnotationSetsResponse) String() string
type SearchAnnotationsRequest struct {
// 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 `protobuf:"bytes,1,rep,name=annotation_set_ids,json=annotationSetIds,proto3" json:"annotation_set_ids,omitempty"`
// Required. `reference_id` or `reference_name` must be set.
//
// Types that are assignable to Reference:
//
// *SearchAnnotationsRequest_ReferenceId
// *SearchAnnotationsRequest_ReferenceName
Reference isSearchAnnotationsRequest_Reference `protobuf_oneof:"reference"`
// The start position of the range on the reference, 0-based inclusive. If
// specified,
// [referenceId][google.genomics.v1.SearchAnnotationsRequest.reference_id] or
// [referenceName][google.genomics.v1.SearchAnnotationsRequest.reference_name]
// must be specified. Defaults to 0.
Start int64 `protobuf:"varint,4,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive. If
// [referenceId][google.genomics.v1.SearchAnnotationsRequest.reference_id] or
// [referenceName][google.genomics.v1.SearchAnnotationsRequest.reference_name]
// must be specified, Defaults to the length of the reference.
End int64 `protobuf:"varint,5,opt,name=end,proto3" json:"end,omitempty"`
// 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 `protobuf:"bytes,6,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 256. The maximum value is 2048.
PageSize int32 `protobuf:"varint,7,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchAnnotationsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchAnnotationsRequest.ProtoReflect.Descriptor instead.
func (x *SearchAnnotationsRequest) GetAnnotationSetIds() []string
func (x *SearchAnnotationsRequest) GetEnd() int64
func (x *SearchAnnotationsRequest) GetPageSize() int32
func (x *SearchAnnotationsRequest) GetPageToken() string
func (m *SearchAnnotationsRequest) GetReference() isSearchAnnotationsRequest_Reference
func (x *SearchAnnotationsRequest) GetReferenceId() string
func (x *SearchAnnotationsRequest) GetReferenceName() string
func (x *SearchAnnotationsRequest) GetStart() int64
func (*SearchAnnotationsRequest) ProtoMessage()
func (x *SearchAnnotationsRequest) ProtoReflect() protoreflect.Message
func (x *SearchAnnotationsRequest) Reset()
func (x *SearchAnnotationsRequest) String() string
type SearchAnnotationsRequest_ReferenceId struct {
// The ID of the reference to query.
ReferenceId string `protobuf:"bytes,2,opt,name=reference_id,json=referenceId,proto3,oneof"`
}
type SearchAnnotationsRequest_ReferenceName struct {
// The name of the reference to query, within the reference set associated
// with this query.
ReferenceName string `protobuf:"bytes,3,opt,name=reference_name,json=referenceName,proto3,oneof"`
}
type SearchAnnotationsResponse struct {
// The matching annotations.
Annotations []*Annotation `protobuf:"bytes,1,rep,name=annotations,proto3" json:"annotations,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchAnnotationsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchAnnotationsResponse.ProtoReflect.Descriptor instead.
func (x *SearchAnnotationsResponse) GetAnnotations() []*Annotation
func (x *SearchAnnotationsResponse) GetNextPageToken() string
func (*SearchAnnotationsResponse) ProtoMessage()
func (x *SearchAnnotationsResponse) ProtoReflect() protoreflect.Message
func (x *SearchAnnotationsResponse) Reset()
func (x *SearchAnnotationsResponse) String() string
The call set search request.
type SearchCallSetsRequest struct {
// Restrict the query to call sets within the given variant sets. At least one
// ID must be provided.
VariantSetIds []string `protobuf:"bytes,1,rep,name=variant_set_ids,json=variantSetIds,proto3" json:"variant_set_ids,omitempty"`
// Only return call sets for which a substring of the name matches this
// string.
Name string `protobuf:"bytes,2,opt,name=name,proto3" json:"name,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024.
PageSize int32 `protobuf:"varint,4,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchCallSetsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchCallSetsRequest.ProtoReflect.Descriptor instead.
func (x *SearchCallSetsRequest) GetName() string
func (x *SearchCallSetsRequest) GetPageSize() int32
func (x *SearchCallSetsRequest) GetPageToken() string
func (x *SearchCallSetsRequest) GetVariantSetIds() []string
func (*SearchCallSetsRequest) ProtoMessage()
func (x *SearchCallSetsRequest) ProtoReflect() protoreflect.Message
func (x *SearchCallSetsRequest) Reset()
func (x *SearchCallSetsRequest) String() string
The call set search response.
type SearchCallSetsResponse struct {
// The list of matching call sets.
CallSets []*CallSet `protobuf:"bytes,1,rep,name=call_sets,json=callSets,proto3" json:"call_sets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchCallSetsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchCallSetsResponse.ProtoReflect.Descriptor instead.
func (x *SearchCallSetsResponse) GetCallSets() []*CallSet
func (x *SearchCallSetsResponse) GetNextPageToken() string
func (*SearchCallSetsResponse) ProtoMessage()
func (x *SearchCallSetsResponse) ProtoReflect() protoreflect.Message
func (x *SearchCallSetsResponse) Reset()
func (x *SearchCallSetsResponse) String() string
The read group set search request.
type SearchReadGroupSetsRequest struct {
// Restricts this query to read group sets within the given datasets. At least
// one ID must be provided.
DatasetIds []string `protobuf:"bytes,1,rep,name=dataset_ids,json=datasetIds,proto3" json:"dataset_ids,omitempty"`
// Only return read group sets for which a substring of the name matches this
// string.
Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 256. The maximum value is 1024.
PageSize int32 `protobuf:"varint,4,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReadGroupSetsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchReadGroupSetsRequest.ProtoReflect.Descriptor instead.
func (x *SearchReadGroupSetsRequest) GetDatasetIds() []string
func (x *SearchReadGroupSetsRequest) GetName() string
func (x *SearchReadGroupSetsRequest) GetPageSize() int32
func (x *SearchReadGroupSetsRequest) GetPageToken() string
func (*SearchReadGroupSetsRequest) ProtoMessage()
func (x *SearchReadGroupSetsRequest) ProtoReflect() protoreflect.Message
func (x *SearchReadGroupSetsRequest) Reset()
func (x *SearchReadGroupSetsRequest) String() string
The read group set search response.
type SearchReadGroupSetsResponse struct {
// The list of matching read group sets.
ReadGroupSets []*ReadGroupSet `protobuf:"bytes,1,rep,name=read_group_sets,json=readGroupSets,proto3" json:"read_group_sets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReadGroupSetsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchReadGroupSetsResponse.ProtoReflect.Descriptor instead.
func (x *SearchReadGroupSetsResponse) GetNextPageToken() string
func (x *SearchReadGroupSetsResponse) GetReadGroupSets() []*ReadGroupSet
func (*SearchReadGroupSetsResponse) ProtoMessage()
func (x *SearchReadGroupSetsResponse) ProtoReflect() protoreflect.Message
func (x *SearchReadGroupSetsResponse) Reset()
func (x *SearchReadGroupSetsResponse) String() string
The read search request.
type SearchReadsRequest struct {
// 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 `protobuf:"bytes,1,rep,name=read_group_set_ids,json=readGroupSetIds,proto3" json:"read_group_set_ids,omitempty"`
// 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 `protobuf:"bytes,5,rep,name=read_group_ids,json=readGroupIds,proto3" json:"read_group_ids,omitempty"`
// 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 `protobuf:"bytes,7,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified.
Start int64 `protobuf:"varint,8,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified.
End int64 `protobuf:"varint,9,opt,name=end,proto3" json:"end,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 256. The maximum value is 2048.
PageSize int32 `protobuf:"varint,4,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReadsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchReadsRequest.ProtoReflect.Descriptor instead.
func (x *SearchReadsRequest) GetEnd() int64
func (x *SearchReadsRequest) GetPageSize() int32
func (x *SearchReadsRequest) GetPageToken() string
func (x *SearchReadsRequest) GetReadGroupIds() []string
func (x *SearchReadsRequest) GetReadGroupSetIds() []string
func (x *SearchReadsRequest) GetReferenceName() string
func (x *SearchReadsRequest) GetStart() int64
func (*SearchReadsRequest) ProtoMessage()
func (x *SearchReadsRequest) ProtoReflect() protoreflect.Message
func (x *SearchReadsRequest) Reset()
func (x *SearchReadsRequest) String() string
The read search response.
type SearchReadsResponse struct {
// 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 `protobuf:"bytes,1,rep,name=alignments,proto3" json:"alignments,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReadsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchReadsResponse.ProtoReflect.Descriptor instead.
func (x *SearchReadsResponse) GetAlignments() []*Read
func (x *SearchReadsResponse) GetNextPageToken() string
func (*SearchReadsResponse) ProtoMessage()
func (x *SearchReadsResponse) ProtoReflect() protoreflect.Message
func (x *SearchReadsResponse) Reset()
func (x *SearchReadsResponse) String() string
type SearchReferenceSetsRequest struct {
// If present, return reference sets for which the
// [md5checksum][google.genomics.v1.ReferenceSet.md5checksum] matches exactly.
Md5Checksums []string `protobuf:"bytes,1,rep,name=md5checksums,proto3" json:"md5checksums,omitempty"`
// If present, return reference sets for which a prefix of any of
// [sourceAccessions][google.genomics.v1.ReferenceSet.source_accessions]
// match any of these strings. Accession numbers typically have a main number
// and a version, for example `NC_000001.11`.
Accessions []string `protobuf:"bytes,2,rep,name=accessions,proto3" json:"accessions,omitempty"`
// If present, return reference sets for which a substring of their
// `assemblyId` matches this string (case insensitive).
AssemblyId string `protobuf:"bytes,3,opt,name=assembly_id,json=assemblyId,proto3" json:"assembly_id,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 4096.
PageSize int32 `protobuf:"varint,5,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReferenceSetsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchReferenceSetsRequest.ProtoReflect.Descriptor instead.
func (x *SearchReferenceSetsRequest) GetAccessions() []string
func (x *SearchReferenceSetsRequest) GetAssemblyId() string
func (x *SearchReferenceSetsRequest) GetMd5Checksums() []string
func (x *SearchReferenceSetsRequest) GetPageSize() int32
func (x *SearchReferenceSetsRequest) GetPageToken() string
func (*SearchReferenceSetsRequest) ProtoMessage()
func (x *SearchReferenceSetsRequest) ProtoReflect() protoreflect.Message
func (x *SearchReferenceSetsRequest) Reset()
func (x *SearchReferenceSetsRequest) String() string
type SearchReferenceSetsResponse struct {
// The matching references sets.
ReferenceSets []*ReferenceSet `protobuf:"bytes,1,rep,name=reference_sets,json=referenceSets,proto3" json:"reference_sets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReferenceSetsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchReferenceSetsResponse.ProtoReflect.Descriptor instead.
func (x *SearchReferenceSetsResponse) GetNextPageToken() string
func (x *SearchReferenceSetsResponse) GetReferenceSets() []*ReferenceSet
func (*SearchReferenceSetsResponse) ProtoMessage()
func (x *SearchReferenceSetsResponse) ProtoReflect() protoreflect.Message
func (x *SearchReferenceSetsResponse) Reset()
func (x *SearchReferenceSetsResponse) String() string
type SearchReferencesRequest struct {
// If present, return references for which the
// [md5checksum][google.genomics.v1.Reference.md5checksum] matches exactly.
Md5Checksums []string `protobuf:"bytes,1,rep,name=md5checksums,proto3" json:"md5checksums,omitempty"`
// If present, return references for which a prefix of any of
// [sourceAccessions][google.genomics.v1.Reference.source_accessions] match
// any of these strings. Accession numbers typically have a main number and a
// version, for example `GCF_000001405.26`.
Accessions []string `protobuf:"bytes,2,rep,name=accessions,proto3" json:"accessions,omitempty"`
// If present, return only references which belong to this reference set.
ReferenceSetId string `protobuf:"bytes,3,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 4096.
PageSize int32 `protobuf:"varint,5,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReferencesRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchReferencesRequest.ProtoReflect.Descriptor instead.
func (x *SearchReferencesRequest) GetAccessions() []string
func (x *SearchReferencesRequest) GetMd5Checksums() []string
func (x *SearchReferencesRequest) GetPageSize() int32
func (x *SearchReferencesRequest) GetPageToken() string
func (x *SearchReferencesRequest) GetReferenceSetId() string
func (*SearchReferencesRequest) ProtoMessage()
func (x *SearchReferencesRequest) ProtoReflect() protoreflect.Message
func (x *SearchReferencesRequest) Reset()
func (x *SearchReferencesRequest) String() string
type SearchReferencesResponse struct {
// The matching references.
References []*Reference `protobuf:"bytes,1,rep,name=references,proto3" json:"references,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchReferencesResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchReferencesResponse.ProtoReflect.Descriptor instead.
func (x *SearchReferencesResponse) GetNextPageToken() string
func (x *SearchReferencesResponse) GetReferences() []*Reference
func (*SearchReferencesResponse) ProtoMessage()
func (x *SearchReferencesResponse) ProtoReflect() protoreflect.Message
func (x *SearchReferencesResponse) Reset()
func (x *SearchReferencesResponse) String() string
The search variant sets request.
type SearchVariantSetsRequest struct {
// Exactly one dataset ID must be provided here. Only variant sets which
// belong to this dataset will be returned.
DatasetIds []string `protobuf:"bytes,1,rep,name=dataset_ids,json=datasetIds,proto3" json:"dataset_ids,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024.
PageSize int32 `protobuf:"varint,3,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// contains filtered or unexported fields
}
func (*SearchVariantSetsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchVariantSetsRequest.ProtoReflect.Descriptor instead.
func (x *SearchVariantSetsRequest) GetDatasetIds() []string
func (x *SearchVariantSetsRequest) GetPageSize() int32
func (x *SearchVariantSetsRequest) GetPageToken() string
func (*SearchVariantSetsRequest) ProtoMessage()
func (x *SearchVariantSetsRequest) ProtoReflect() protoreflect.Message
func (x *SearchVariantSetsRequest) Reset()
func (x *SearchVariantSetsRequest) String() string
The search variant sets response.
type SearchVariantSetsResponse struct {
// The variant sets belonging to the requested dataset.
VariantSets []*VariantSet `protobuf:"bytes,1,rep,name=variant_sets,json=variantSets,proto3" json:"variant_sets,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchVariantSetsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchVariantSetsResponse.ProtoReflect.Descriptor instead.
func (x *SearchVariantSetsResponse) GetNextPageToken() string
func (x *SearchVariantSetsResponse) GetVariantSets() []*VariantSet
func (*SearchVariantSetsResponse) ProtoMessage()
func (x *SearchVariantSetsResponse) ProtoReflect() protoreflect.Message
func (x *SearchVariantSetsResponse) Reset()
func (x *SearchVariantSetsResponse) String() string
The variant search request.
type SearchVariantsRequest struct {
// 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 `protobuf:"bytes,1,rep,name=variant_set_ids,json=variantSetIds,proto3" json:"variant_set_ids,omitempty"`
// Only return variants which have exactly this name.
VariantName string `protobuf:"bytes,2,opt,name=variant_name,json=variantName,proto3" json:"variant_name,omitempty"`
// 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 `protobuf:"bytes,3,rep,name=call_set_ids,json=callSetIds,proto3" json:"call_set_ids,omitempty"`
// Required. Only return variants in this reference sequence.
ReferenceName string `protobuf:"bytes,4,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The beginning of the window (0-based, inclusive) for which
// overlapping variants should be returned. If unspecified, defaults to 0.
Start int64 `protobuf:"varint,5,opt,name=start,proto3" json:"start,omitempty"`
// The end of the window, 0-based exclusive. If unspecified or 0, defaults to
// the length of the reference.
End int64 `protobuf:"varint,6,opt,name=end,proto3" json:"end,omitempty"`
// 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 `protobuf:"bytes,7,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"`
// The maximum number of variants to return in a single page. If unspecified,
// defaults to 5000. The maximum value is 10000.
PageSize int32 `protobuf:"varint,8,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"`
// 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 int32 `protobuf:"varint,9,opt,name=max_calls,json=maxCalls,proto3" json:"max_calls,omitempty"`
// contains filtered or unexported fields
}
func (*SearchVariantsRequest) Descriptor() ([]byte, []int)
Deprecated: Use SearchVariantsRequest.ProtoReflect.Descriptor instead.
func (x *SearchVariantsRequest) GetCallSetIds() []string
func (x *SearchVariantsRequest) GetEnd() int64
func (x *SearchVariantsRequest) GetMaxCalls() int32
func (x *SearchVariantsRequest) GetPageSize() int32
func (x *SearchVariantsRequest) GetPageToken() string
func (x *SearchVariantsRequest) GetReferenceName() string
func (x *SearchVariantsRequest) GetStart() int64
func (x *SearchVariantsRequest) GetVariantName() string
func (x *SearchVariantsRequest) GetVariantSetIds() []string
func (*SearchVariantsRequest) ProtoMessage()
func (x *SearchVariantsRequest) ProtoReflect() protoreflect.Message
func (x *SearchVariantsRequest) Reset()
func (x *SearchVariantsRequest) String() string
The variant search response.
type SearchVariantsResponse struct {
// The list of matching Variants.
Variants []*Variant `protobuf:"bytes,1,rep,name=variants,proto3" json:"variants,omitempty"`
// 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 `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"`
// contains filtered or unexported fields
}
func (*SearchVariantsResponse) Descriptor() ([]byte, []int)
Deprecated: Use SearchVariantsResponse.ProtoReflect.Descriptor instead.
func (x *SearchVariantsResponse) GetNextPageToken() string
func (x *SearchVariantsResponse) GetVariants() []*Variant
func (*SearchVariantsResponse) ProtoMessage()
func (x *SearchVariantsResponse) ProtoReflect() protoreflect.Message
func (x *SearchVariantsResponse) Reset()
func (x *SearchVariantsResponse) String() string
The stream reads request.
type StreamReadsRequest struct {
// The Google Cloud project ID which will be billed
// for this access. The caller must have WRITE access to this project.
// Required.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// The ID of the read group set from which to stream reads.
ReadGroupSetId string `protobuf:"bytes,2,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The reference sequence name, for example `chr1`,
// `1`, or `chrX`. If set to *, only unmapped reads are
// returned.
ReferenceName string `protobuf:"bytes,3,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified.
Start int64 `protobuf:"varint,4,opt,name=start,proto3" json:"start,omitempty"`
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified.
End int64 `protobuf:"varint,5,opt,name=end,proto3" json:"end,omitempty"`
// Restricts results to a shard containing approximately `1/totalShards`
// of the normal response payload for this query. Results from a sharded
// request are disjoint from those returned by all queries which differ only
// in their shard parameter. A shard may yield 0 results; this is especially
// likely for large values of `totalShards`.
//
// Valid values are `[0, totalShards)`.
Shard int32 `protobuf:"varint,6,opt,name=shard,proto3" json:"shard,omitempty"`
// Specifying `totalShards` causes a disjoint subset of the normal response
// payload to be returned for each query with a unique `shard` parameter
// specified. A best effort is made to yield equally sized shards. Sharding
// can be used to distribute processing amongst workers, where each worker is
// assigned a unique `shard` number and all workers specify the same
// `totalShards` number. The union of reads returned for all sharded queries
// `[0, totalShards)` is equal to those returned by a single unsharded query.
//
// Queries for different values of `totalShards` with common divisors will
// share shard boundaries. For example, streaming `shard` 2 of 5
// `totalShards` yields the same results as streaming `shard`s 4 and 5 of 10
// `totalShards`. This property can be leveraged for adaptive retries.
TotalShards int32 `protobuf:"varint,7,opt,name=total_shards,json=totalShards,proto3" json:"total_shards,omitempty"`
// contains filtered or unexported fields
}
func (*StreamReadsRequest) Descriptor() ([]byte, []int)
Deprecated: Use StreamReadsRequest.ProtoReflect.Descriptor instead.
func (x *StreamReadsRequest) GetEnd() int64
func (x *StreamReadsRequest) GetProjectId() string
func (x *StreamReadsRequest) GetReadGroupSetId() string
func (x *StreamReadsRequest) GetReferenceName() string
func (x *StreamReadsRequest) GetShard() int32
func (x *StreamReadsRequest) GetStart() int64
func (x *StreamReadsRequest) GetTotalShards() int32
func (*StreamReadsRequest) ProtoMessage()
func (x *StreamReadsRequest) ProtoReflect() protoreflect.Message
func (x *StreamReadsRequest) Reset()
func (x *StreamReadsRequest) String() string
type StreamReadsResponse struct {
Alignments []*Read `protobuf:"bytes,1,rep,name=alignments,proto3" json:"alignments,omitempty"`
// contains filtered or unexported fields
}
func (*StreamReadsResponse) Descriptor() ([]byte, []int)
Deprecated: Use StreamReadsResponse.ProtoReflect.Descriptor instead.
func (x *StreamReadsResponse) GetAlignments() []*Read
func (*StreamReadsResponse) ProtoMessage()
func (x *StreamReadsResponse) ProtoReflect() protoreflect.Message
func (x *StreamReadsResponse) Reset()
func (x *StreamReadsResponse) String() string
The stream variants request.
type StreamVariantsRequest struct {
// The Google Cloud project ID which will be billed
// for this access. The caller must have WRITE access to this project.
// Required.
ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"`
// The variant set ID from which to stream variants.
VariantSetId string `protobuf:"bytes,2,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// Only return variant calls which belong to call sets with these IDs.
// Leaving this blank returns all variant calls.
CallSetIds []string `protobuf:"bytes,3,rep,name=call_set_ids,json=callSetIds,proto3" json:"call_set_ids,omitempty"`
// Required. Only return variants in this reference sequence.
ReferenceName string `protobuf:"bytes,4,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The beginning of the window (0-based, inclusive) for which
// overlapping variants should be returned.
Start int64 `protobuf:"varint,5,opt,name=start,proto3" json:"start,omitempty"`
// The end of the window (0-based, exclusive) for which overlapping
// variants should be returned.
End int64 `protobuf:"varint,6,opt,name=end,proto3" json:"end,omitempty"`
// contains filtered or unexported fields
}
func (*StreamVariantsRequest) Descriptor() ([]byte, []int)
Deprecated: Use StreamVariantsRequest.ProtoReflect.Descriptor instead.
func (x *StreamVariantsRequest) GetCallSetIds() []string
func (x *StreamVariantsRequest) GetEnd() int64
func (x *StreamVariantsRequest) GetProjectId() string
func (x *StreamVariantsRequest) GetReferenceName() string
func (x *StreamVariantsRequest) GetStart() int64
func (x *StreamVariantsRequest) GetVariantSetId() string
func (*StreamVariantsRequest) ProtoMessage()
func (x *StreamVariantsRequest) ProtoReflect() protoreflect.Message
func (x *StreamVariantsRequest) Reset()
func (x *StreamVariantsRequest) String() string
type StreamVariantsResponse struct {
Variants []*Variant `protobuf:"bytes,1,rep,name=variants,proto3" json:"variants,omitempty"`
// contains filtered or unexported fields
}
func (*StreamVariantsResponse) Descriptor() ([]byte, []int)
Deprecated: Use StreamVariantsResponse.ProtoReflect.Descriptor instead.
func (x *StreamVariantsResponse) GetVariants() []*Variant
func (*StreamVariantsResponse) ProtoMessage()
func (x *StreamVariantsResponse) ProtoReflect() protoreflect.Message
func (x *StreamVariantsResponse) Reset()
func (x *StreamVariantsResponse) String() string
StreamingReadServiceClient is the client API for StreamingReadService service.
For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.
type StreamingReadServiceClient interface {
// Returns a stream of all the reads matching the search request, ordered
// by reference name, position, and ID.
StreamReads(ctx context.Context, in *StreamReadsRequest, opts ...grpc.CallOption) (StreamingReadService_StreamReadsClient, error)
}
func NewStreamingReadServiceClient(cc grpc.ClientConnInterface) StreamingReadServiceClient
StreamingReadServiceServer is the server API for StreamingReadService service.
type StreamingReadServiceServer interface {
// Returns a stream of all the reads matching the search request, ordered
// by reference name, position, and ID.
StreamReads(*StreamReadsRequest, StreamingReadService_StreamReadsServer) error
}
type StreamingReadService_StreamReadsClient interface {
Recv() (*StreamReadsResponse, error)
grpc.ClientStream
}
type StreamingReadService_StreamReadsServer interface {
Send(*StreamReadsResponse) error
grpc.ServerStream
}
StreamingVariantServiceClient is the client API for StreamingVariantService service.
For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.
type StreamingVariantServiceClient interface {
// Returns a stream of all the variants matching the search request, ordered
// by reference name, position, and ID.
StreamVariants(ctx context.Context, in *StreamVariantsRequest, opts ...grpc.CallOption) (StreamingVariantService_StreamVariantsClient, error)
}
func NewStreamingVariantServiceClient(cc grpc.ClientConnInterface) StreamingVariantServiceClient
StreamingVariantServiceServer is the server API for StreamingVariantService service.
type StreamingVariantServiceServer interface {
// Returns a stream of all the variants matching the search request, ordered
// by reference name, position, and ID.
StreamVariants(*StreamVariantsRequest, StreamingVariantService_StreamVariantsServer) error
}
type StreamingVariantService_StreamVariantsClient interface {
Recv() (*StreamVariantsResponse, error)
grpc.ClientStream
}
type StreamingVariantService_StreamVariantsServer interface {
Send(*StreamVariantsResponse) error
grpc.ServerStream
}
A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA.
type Transcript struct {
// The annotation ID of the gene from which this transcript is transcribed.
GeneId string `protobuf:"bytes,1,opt,name=gene_id,json=geneId,proto3" json:"gene_id,omitempty"`
// 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][google.genomics.v1.Transcript.coding_sequence] correspond
// to coding DNA sequence.
//
// Exons are ordered by start position and may not overlap.
Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"`
// 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][google.genomics.v1.Transcript.exons], if any. If there are any
// [exons][google.genomics.v1.Transcript.exons], the
// [codingSequence][google.genomics.v1.Transcript.coding_sequence] 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][google.genomics.v1.Transcript.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 *Transcript_CodingSequence `protobuf:"bytes,3,opt,name=coding_sequence,json=codingSequence,proto3" json:"coding_sequence,omitempty"`
// contains filtered or unexported fields
}
func (*Transcript) Descriptor() ([]byte, []int)
Deprecated: Use Transcript.ProtoReflect.Descriptor instead.
func (x *Transcript) GetCodingSequence() *Transcript_CodingSequence
func (x *Transcript) GetExons() []*Transcript_Exon
func (x *Transcript) GetGeneId() string
func (*Transcript) ProtoMessage()
func (x *Transcript) ProtoReflect() protoreflect.Message
func (x *Transcript) Reset()
func (x *Transcript) String() string
type Transcript_CodingSequence struct {
// 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 `protobuf:"varint,1,opt,name=start,proto3" json:"start,omitempty"`
// 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 `protobuf:"varint,2,opt,name=end,proto3" json:"end,omitempty"`
// contains filtered or unexported fields
}
func (*Transcript_CodingSequence) Descriptor() ([]byte, []int)
Deprecated: Use Transcript_CodingSequence.ProtoReflect.Descriptor instead.
func (x *Transcript_CodingSequence) GetEnd() int64
func (x *Transcript_CodingSequence) GetStart() int64
func (*Transcript_CodingSequence) ProtoMessage()
func (x *Transcript_CodingSequence) ProtoReflect() protoreflect.Message
func (x *Transcript_CodingSequence) Reset()
func (x *Transcript_CodingSequence) String() string
type Transcript_Exon struct {
// 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 `protobuf:"varint,1,opt,name=start,proto3" json:"start,omitempty"`
// 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 `protobuf:"varint,2,opt,name=end,proto3" json:"end,omitempty"`
// 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][google.genomics.v1.Annotation.reverse_strand]).
// For forward stranded annotations, this offset is relative to the
// [exon.start][google.genomics.v1.Transcript.Exon.start]. For reverse
// strand annotations, this offset is relative to the
// [exon.end][google.genomics.v1.Transcript.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 *wrapperspb.Int32Value `protobuf:"bytes,3,opt,name=frame,proto3" json:"frame,omitempty"`
// contains filtered or unexported fields
}
func (*Transcript_Exon) Descriptor() ([]byte, []int)
Deprecated: Use Transcript_Exon.ProtoReflect.Descriptor instead.
func (x *Transcript_Exon) GetEnd() int64
func (x *Transcript_Exon) GetFrame() *wrapperspb.Int32Value
func (x *Transcript_Exon) GetStart() int64
func (*Transcript_Exon) ProtoMessage()
func (x *Transcript_Exon) ProtoReflect() protoreflect.Message
func (x *Transcript_Exon) Reset()
func (x *Transcript_Exon) String() string
type UndeleteDatasetRequest struct {
// The ID of the dataset to be undeleted.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// contains filtered or unexported fields
}
func (*UndeleteDatasetRequest) Descriptor() ([]byte, []int)
Deprecated: Use UndeleteDatasetRequest.ProtoReflect.Descriptor instead.
func (x *UndeleteDatasetRequest) GetDatasetId() string
func (*UndeleteDatasetRequest) ProtoMessage()
func (x *UndeleteDatasetRequest) ProtoReflect() protoreflect.Message
func (x *UndeleteDatasetRequest) Reset()
func (x *UndeleteDatasetRequest) String() string
UnimplementedAnnotationServiceV1Server can be embedded to have forward compatible implementations.
type UnimplementedAnnotationServiceV1Server struct {
}
func (*UnimplementedAnnotationServiceV1Server) BatchCreateAnnotations(context.Context, *BatchCreateAnnotationsRequest) (*BatchCreateAnnotationsResponse, error)
func (*UnimplementedAnnotationServiceV1Server) CreateAnnotation(context.Context, *CreateAnnotationRequest) (*Annotation, error)
func (*UnimplementedAnnotationServiceV1Server) CreateAnnotationSet(context.Context, *CreateAnnotationSetRequest) (*AnnotationSet, error)
func (*UnimplementedAnnotationServiceV1Server) DeleteAnnotation(context.Context, *DeleteAnnotationRequest) (*emptypb.Empty, error)
func (*UnimplementedAnnotationServiceV1Server) DeleteAnnotationSet(context.Context, *DeleteAnnotationSetRequest) (*emptypb.Empty, error)
func (*UnimplementedAnnotationServiceV1Server) GetAnnotation(context.Context, *GetAnnotationRequest) (*Annotation, error)
func (*UnimplementedAnnotationServiceV1Server) GetAnnotationSet(context.Context, *GetAnnotationSetRequest) (*AnnotationSet, error)
func (*UnimplementedAnnotationServiceV1Server) SearchAnnotationSets(context.Context, *SearchAnnotationSetsRequest) (*SearchAnnotationSetsResponse, error)
func (*UnimplementedAnnotationServiceV1Server) SearchAnnotations(context.Context, *SearchAnnotationsRequest) (*SearchAnnotationsResponse, error)
func (*UnimplementedAnnotationServiceV1Server) UpdateAnnotation(context.Context, *UpdateAnnotationRequest) (*Annotation, error)
func (*UnimplementedAnnotationServiceV1Server) UpdateAnnotationSet(context.Context, *UpdateAnnotationSetRequest) (*AnnotationSet, error)
UnimplementedDatasetServiceV1Server can be embedded to have forward compatible implementations.
type UnimplementedDatasetServiceV1Server struct {
}
func (*UnimplementedDatasetServiceV1Server) CreateDataset(context.Context, *CreateDatasetRequest) (*Dataset, error)
func (*UnimplementedDatasetServiceV1Server) DeleteDataset(context.Context, *DeleteDatasetRequest) (*emptypb.Empty, error)
func (*UnimplementedDatasetServiceV1Server) GetDataset(context.Context, *GetDatasetRequest) (*Dataset, error)
func (*UnimplementedDatasetServiceV1Server) GetIamPolicy(context.Context, *iampb.GetIamPolicyRequest) (*iampb.Policy, error)
func (*UnimplementedDatasetServiceV1Server) ListDatasets(context.Context, *ListDatasetsRequest) (*ListDatasetsResponse, error)
func (*UnimplementedDatasetServiceV1Server) SetIamPolicy(context.Context, *iampb.SetIamPolicyRequest) (*iampb.Policy, error)
func (*UnimplementedDatasetServiceV1Server) TestIamPermissions(context.Context, *iampb.TestIamPermissionsRequest) (*iampb.TestIamPermissionsResponse, error)
func (*UnimplementedDatasetServiceV1Server) UndeleteDataset(context.Context, *UndeleteDatasetRequest) (*Dataset, error)
func (*UnimplementedDatasetServiceV1Server) UpdateDataset(context.Context, *UpdateDatasetRequest) (*Dataset, error)
UnimplementedReadServiceV1Server can be embedded to have forward compatible implementations.
type UnimplementedReadServiceV1Server struct {
}
func (*UnimplementedReadServiceV1Server) DeleteReadGroupSet(context.Context, *DeleteReadGroupSetRequest) (*emptypb.Empty, error)
func (*UnimplementedReadServiceV1Server) ExportReadGroupSet(context.Context, *ExportReadGroupSetRequest) (*longrunningpb.Operation, error)
func (*UnimplementedReadServiceV1Server) GetReadGroupSet(context.Context, *GetReadGroupSetRequest) (*ReadGroupSet, error)
func (*UnimplementedReadServiceV1Server) ImportReadGroupSets(context.Context, *ImportReadGroupSetsRequest) (*longrunningpb.Operation, error)
func (*UnimplementedReadServiceV1Server) ListCoverageBuckets(context.Context, *ListCoverageBucketsRequest) (*ListCoverageBucketsResponse, error)
func (*UnimplementedReadServiceV1Server) SearchReadGroupSets(context.Context, *SearchReadGroupSetsRequest) (*SearchReadGroupSetsResponse, error)
func (*UnimplementedReadServiceV1Server) SearchReads(context.Context, *SearchReadsRequest) (*SearchReadsResponse, error)
func (*UnimplementedReadServiceV1Server) UpdateReadGroupSet(context.Context, *UpdateReadGroupSetRequest) (*ReadGroupSet, error)
UnimplementedReferenceServiceV1Server can be embedded to have forward compatible implementations.
type UnimplementedReferenceServiceV1Server struct {
}
func (*UnimplementedReferenceServiceV1Server) GetReference(context.Context, *GetReferenceRequest) (*Reference, error)
func (*UnimplementedReferenceServiceV1Server) GetReferenceSet(context.Context, *GetReferenceSetRequest) (*ReferenceSet, error)
func (*UnimplementedReferenceServiceV1Server) ListBases(context.Context, *ListBasesRequest) (*ListBasesResponse, error)
func (*UnimplementedReferenceServiceV1Server) SearchReferenceSets(context.Context, *SearchReferenceSetsRequest) (*SearchReferenceSetsResponse, error)
func (*UnimplementedReferenceServiceV1Server) SearchReferences(context.Context, *SearchReferencesRequest) (*SearchReferencesResponse, error)
UnimplementedStreamingReadServiceServer can be embedded to have forward compatible implementations.
type UnimplementedStreamingReadServiceServer struct {
}
func (*UnimplementedStreamingReadServiceServer) StreamReads(*StreamReadsRequest, StreamingReadService_StreamReadsServer) error
UnimplementedStreamingVariantServiceServer can be embedded to have forward compatible implementations.
type UnimplementedStreamingVariantServiceServer struct {
}
func (*UnimplementedStreamingVariantServiceServer) StreamVariants(*StreamVariantsRequest, StreamingVariantService_StreamVariantsServer) error
UnimplementedVariantServiceV1Server can be embedded to have forward compatible implementations.
type UnimplementedVariantServiceV1Server struct {
}
func (*UnimplementedVariantServiceV1Server) CreateCallSet(context.Context, *CreateCallSetRequest) (*CallSet, error)
func (*UnimplementedVariantServiceV1Server) CreateVariant(context.Context, *CreateVariantRequest) (*Variant, error)
func (*UnimplementedVariantServiceV1Server) CreateVariantSet(context.Context, *CreateVariantSetRequest) (*VariantSet, error)
func (*UnimplementedVariantServiceV1Server) DeleteCallSet(context.Context, *DeleteCallSetRequest) (*emptypb.Empty, error)
func (*UnimplementedVariantServiceV1Server) DeleteVariant(context.Context, *DeleteVariantRequest) (*emptypb.Empty, error)
func (*UnimplementedVariantServiceV1Server) DeleteVariantSet(context.Context, *DeleteVariantSetRequest) (*emptypb.Empty, error)
func (*UnimplementedVariantServiceV1Server) ExportVariantSet(context.Context, *ExportVariantSetRequest) (*longrunningpb.Operation, error)
func (*UnimplementedVariantServiceV1Server) GetCallSet(context.Context, *GetCallSetRequest) (*CallSet, error)
func (*UnimplementedVariantServiceV1Server) GetVariant(context.Context, *GetVariantRequest) (*Variant, error)
func (*UnimplementedVariantServiceV1Server) GetVariantSet(context.Context, *GetVariantSetRequest) (*VariantSet, error)
func (*UnimplementedVariantServiceV1Server) ImportVariants(context.Context, *ImportVariantsRequest) (*longrunningpb.Operation, error)
func (*UnimplementedVariantServiceV1Server) MergeVariants(context.Context, *MergeVariantsRequest) (*emptypb.Empty, error)
func (*UnimplementedVariantServiceV1Server) SearchCallSets(context.Context, *SearchCallSetsRequest) (*SearchCallSetsResponse, error)
func (*UnimplementedVariantServiceV1Server) SearchVariantSets(context.Context, *SearchVariantSetsRequest) (*SearchVariantSetsResponse, error)
func (*UnimplementedVariantServiceV1Server) SearchVariants(context.Context, *SearchVariantsRequest) (*SearchVariantsResponse, error)
func (*UnimplementedVariantServiceV1Server) UpdateCallSet(context.Context, *UpdateCallSetRequest) (*CallSet, error)
func (*UnimplementedVariantServiceV1Server) UpdateVariant(context.Context, *UpdateVariantRequest) (*Variant, error)
func (*UnimplementedVariantServiceV1Server) UpdateVariantSet(context.Context, *UpdateVariantSetRequest) (*VariantSet, error)
type UpdateAnnotationRequest struct {
// The ID of the annotation to be updated.
AnnotationId string `protobuf:"bytes,1,opt,name=annotation_id,json=annotationId,proto3" json:"annotation_id,omitempty"`
// The new annotation.
Annotation *Annotation `protobuf:"bytes,2,opt,name=annotation,proto3" json:"annotation,omitempty"`
// An optional mask specifying which fields to update. Mutable fields are
// [name][google.genomics.v1.Annotation.name],
// [variant][google.genomics.v1.Annotation.variant],
// [transcript][google.genomics.v1.Annotation.transcript], and
// [info][google.genomics.v1.Annotation.info]. If unspecified, all mutable
// fields will be updated.
UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
// contains filtered or unexported fields
}
func (*UpdateAnnotationRequest) Descriptor() ([]byte, []int)
Deprecated: Use UpdateAnnotationRequest.ProtoReflect.Descriptor instead.
func (x *UpdateAnnotationRequest) GetAnnotation() *Annotation
func (x *UpdateAnnotationRequest) GetAnnotationId() string
func (x *UpdateAnnotationRequest) GetUpdateMask() *fieldmaskpb.FieldMask
func (*UpdateAnnotationRequest) ProtoMessage()
func (x *UpdateAnnotationRequest) ProtoReflect() protoreflect.Message
func (x *UpdateAnnotationRequest) Reset()
func (x *UpdateAnnotationRequest) String() string
type UpdateAnnotationSetRequest struct {
// The ID of the annotation set to be updated.
AnnotationSetId string `protobuf:"bytes,1,opt,name=annotation_set_id,json=annotationSetId,proto3" json:"annotation_set_id,omitempty"`
// The new annotation set.
AnnotationSet *AnnotationSet `protobuf:"bytes,2,opt,name=annotation_set,json=annotationSet,proto3" json:"annotation_set,omitempty"`
// An optional mask specifying which fields to update. Mutable fields are
// [name][google.genomics.v1.AnnotationSet.name],
// [source_uri][google.genomics.v1.AnnotationSet.source_uri], and
// [info][google.genomics.v1.AnnotationSet.info]. If unspecified, all
// mutable fields will be updated.
UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
// contains filtered or unexported fields
}
func (*UpdateAnnotationSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use UpdateAnnotationSetRequest.ProtoReflect.Descriptor instead.
func (x *UpdateAnnotationSetRequest) GetAnnotationSet() *AnnotationSet
func (x *UpdateAnnotationSetRequest) GetAnnotationSetId() string
func (x *UpdateAnnotationSetRequest) GetUpdateMask() *fieldmaskpb.FieldMask
func (*UpdateAnnotationSetRequest) ProtoMessage()
func (x *UpdateAnnotationSetRequest) ProtoReflect() protoreflect.Message
func (x *UpdateAnnotationSetRequest) Reset()
func (x *UpdateAnnotationSetRequest) String() string
type UpdateCallSetRequest struct {
// The ID of the call set to be updated.
CallSetId string `protobuf:"bytes,1,opt,name=call_set_id,json=callSetId,proto3" json:"call_set_id,omitempty"`
// The new call set data.
CallSet *CallSet `protobuf:"bytes,2,opt,name=call_set,json=callSet,proto3" json:"call_set,omitempty"`
// An optional mask specifying which fields to update. At this time, the only
// mutable field is [name][google.genomics.v1.CallSet.name]. The only
// acceptable value is "name". If unspecified, all mutable fields will be
// updated.
UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
// contains filtered or unexported fields
}
func (*UpdateCallSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use UpdateCallSetRequest.ProtoReflect.Descriptor instead.
func (x *UpdateCallSetRequest) GetCallSet() *CallSet
func (x *UpdateCallSetRequest) GetCallSetId() string
func (x *UpdateCallSetRequest) GetUpdateMask() *fieldmaskpb.FieldMask
func (*UpdateCallSetRequest) ProtoMessage()
func (x *UpdateCallSetRequest) ProtoReflect() protoreflect.Message
func (x *UpdateCallSetRequest) Reset()
func (x *UpdateCallSetRequest) String() string
type UpdateDatasetRequest struct {
// The ID of the dataset to be updated.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// The new dataset data.
Dataset *Dataset `protobuf:"bytes,2,opt,name=dataset,proto3" json:"dataset,omitempty"`
// An optional mask specifying which fields to update. At this time, the only
// mutable field is [name][google.genomics.v1.Dataset.name]. The only
// acceptable value is "name". If unspecified, all mutable fields will be
// updated.
UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
// contains filtered or unexported fields
}
func (*UpdateDatasetRequest) Descriptor() ([]byte, []int)
Deprecated: Use UpdateDatasetRequest.ProtoReflect.Descriptor instead.
func (x *UpdateDatasetRequest) GetDataset() *Dataset
func (x *UpdateDatasetRequest) GetDatasetId() string
func (x *UpdateDatasetRequest) GetUpdateMask() *fieldmaskpb.FieldMask
func (*UpdateDatasetRequest) ProtoMessage()
func (x *UpdateDatasetRequest) ProtoReflect() protoreflect.Message
func (x *UpdateDatasetRequest) Reset()
func (x *UpdateDatasetRequest) String() string
type UpdateReadGroupSetRequest struct {
// The ID of the read group set to be updated. The caller must have WRITE
// permissions to the dataset associated with this read group set.
ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
// The new read group set data. See `updateMask` for details on mutability of
// fields.
ReadGroupSet *ReadGroupSet `protobuf:"bytes,2,opt,name=read_group_set,json=readGroupSet,proto3" json:"read_group_set,omitempty"`
// An optional mask specifying which fields to update. Supported fields:
//
// * [name][google.genomics.v1.ReadGroupSet.name].
// * [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id].
//
// Leaving `updateMask` unset is equivalent to specifying all mutable
// fields.
UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
// contains filtered or unexported fields
}
func (*UpdateReadGroupSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use UpdateReadGroupSetRequest.ProtoReflect.Descriptor instead.
func (x *UpdateReadGroupSetRequest) GetReadGroupSet() *ReadGroupSet
func (x *UpdateReadGroupSetRequest) GetReadGroupSetId() string
func (x *UpdateReadGroupSetRequest) GetUpdateMask() *fieldmaskpb.FieldMask
func (*UpdateReadGroupSetRequest) ProtoMessage()
func (x *UpdateReadGroupSetRequest) ProtoReflect() protoreflect.Message
func (x *UpdateReadGroupSetRequest) Reset()
func (x *UpdateReadGroupSetRequest) String() string
type UpdateVariantRequest struct {
// The ID of the variant to be updated.
VariantId string `protobuf:"bytes,1,opt,name=variant_id,json=variantId,proto3" json:"variant_id,omitempty"`
// The new variant data.
Variant *Variant `protobuf:"bytes,2,opt,name=variant,proto3" json:"variant,omitempty"`
// An optional mask specifying which fields to update. At this time, mutable
// fields are [names][google.genomics.v1.Variant.names] and
// [info][google.genomics.v1.Variant.info]. Acceptable values are "names" and
// "info". If unspecified, all mutable fields will be updated.
UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
// contains filtered or unexported fields
}
func (*UpdateVariantRequest) Descriptor() ([]byte, []int)
Deprecated: Use UpdateVariantRequest.ProtoReflect.Descriptor instead.
func (x *UpdateVariantRequest) GetUpdateMask() *fieldmaskpb.FieldMask
func (x *UpdateVariantRequest) GetVariant() *Variant
func (x *UpdateVariantRequest) GetVariantId() string
func (*UpdateVariantRequest) ProtoMessage()
func (x *UpdateVariantRequest) ProtoReflect() protoreflect.Message
func (x *UpdateVariantRequest) Reset()
func (x *UpdateVariantRequest) String() string
type UpdateVariantSetRequest struct {
// The ID of the variant to be updated (must already exist).
VariantSetId string `protobuf:"bytes,1,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// The new variant data. Only the variant_set.metadata will be considered
// for update.
VariantSet *VariantSet `protobuf:"bytes,2,opt,name=variant_set,json=variantSet,proto3" json:"variant_set,omitempty"`
// An optional mask specifying which fields to update. Supported fields:
//
// * [metadata][google.genomics.v1.VariantSet.metadata].
// * [name][google.genomics.v1.VariantSet.name].
// * [description][google.genomics.v1.VariantSet.description].
//
// Leaving `updateMask` unset is equivalent to specifying all mutable
// fields.
UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,5,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"`
// contains filtered or unexported fields
}
func (*UpdateVariantSetRequest) Descriptor() ([]byte, []int)
Deprecated: Use UpdateVariantSetRequest.ProtoReflect.Descriptor instead.
func (x *UpdateVariantSetRequest) GetUpdateMask() *fieldmaskpb.FieldMask
func (x *UpdateVariantSetRequest) GetVariantSet() *VariantSet
func (x *UpdateVariantSetRequest) GetVariantSetId() string
func (*UpdateVariantSetRequest) ProtoMessage()
func (x *UpdateVariantSetRequest) ProtoReflect() protoreflect.Message
func (x *UpdateVariantSetRequest) Reset()
func (x *UpdateVariantSetRequest) String() string
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-google-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 {
// The ID of the variant set this variant belongs to.
VariantSetId string `protobuf:"bytes,15,opt,name=variant_set_id,json=variantSetId,proto3" json:"variant_set_id,omitempty"`
// The server-generated variant ID, unique across all variants.
Id string `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
// Names for the variant, for example a RefSNP ID.
Names []string `protobuf:"bytes,3,rep,name=names,proto3" json:"names,omitempty"`
// The date this variant was created, in milliseconds from the epoch.
Created int64 `protobuf:"varint,12,opt,name=created,proto3" json:"created,omitempty"`
// The reference on which this variant occurs.
// (such as `chr20` or `X`)
ReferenceName string `protobuf:"bytes,14,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"`
// The position at which this variant occurs (0-based).
// This corresponds to the first base of the string of reference bases.
Start int64 `protobuf:"varint,16,opt,name=start,proto3" json:"start,omitempty"`
// 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 `protobuf:"varint,13,opt,name=end,proto3" json:"end,omitempty"`
// The reference bases for this variant. They start at the given
// position.
ReferenceBases string `protobuf:"bytes,6,opt,name=reference_bases,json=referenceBases,proto3" json:"reference_bases,omitempty"`
// The bases that appear instead of the reference bases.
AlternateBases []string `protobuf:"bytes,7,rep,name=alternate_bases,json=alternateBases,proto3" json:"alternate_bases,omitempty"`
// A measure of how likely this variant is to be real.
// A higher value is better.
Quality float64 `protobuf:"fixed64,8,opt,name=quality,proto3" json:"quality,omitempty"`
// A list of filters (normally quality filters) this variant has failed.
// `PASS` indicates this variant has passed all filters.
Filter []string `protobuf:"bytes,9,rep,name=filter,proto3" json:"filter,omitempty"`
// 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]*structpb.ListValue `protobuf:"bytes,10,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// The variant calls for this particular variant. Each one represents the
// determination of genotype with respect to this variant.
Calls []*VariantCall `protobuf:"bytes,11,rep,name=calls,proto3" json:"calls,omitempty"`
// contains filtered or unexported fields
}
func (*Variant) Descriptor() ([]byte, []int)
Deprecated: Use Variant.ProtoReflect.Descriptor instead.
func (x *Variant) GetAlternateBases() []string
func (x *Variant) GetCalls() []*VariantCall
func (x *Variant) GetCreated() int64
func (x *Variant) GetEnd() int64
func (x *Variant) GetFilter() []string
func (x *Variant) GetId() string
func (x *Variant) GetInfo() map[string]*structpb.ListValue
func (x *Variant) GetNames() []string
func (x *Variant) GetQuality() float64
func (x *Variant) GetReferenceBases() string
func (x *Variant) GetReferenceName() string
func (x *Variant) GetStart() int64
func (x *Variant) GetVariantSetId() string
func (*Variant) ProtoMessage()
func (x *Variant) ProtoReflect() protoreflect.Message
func (x *Variant) Reset()
func (x *Variant) String() string
type VariantAnnotation struct {
// Type has been adapted from ClinVar's list of variant types.
Type VariantAnnotation_Type `protobuf:"varint,1,opt,name=type,proto3,enum=google.genomics.v1.VariantAnnotation_Type" json:"type,omitempty"`
// Effect of the variant on the coding sequence.
Effect VariantAnnotation_Effect `protobuf:"varint,2,opt,name=effect,proto3,enum=google.genomics.v1.VariantAnnotation_Effect" json:"effect,omitempty"`
// 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 `protobuf:"bytes,3,opt,name=alternate_bases,json=alternateBases,proto3" json:"alternate_bases,omitempty"`
// Google annotation ID of the gene affected by this variant. This should
// be provided when the variant is created.
GeneId string `protobuf:"bytes,4,opt,name=gene_id,json=geneId,proto3" json:"gene_id,omitempty"`
// Google annotation IDs of the transcripts affected by this variant. These
// should be provided when the variant is created.
TranscriptIds []string `protobuf:"bytes,5,rep,name=transcript_ids,json=transcriptIds,proto3" json:"transcript_ids,omitempty"`
// The set of conditions associated with this variant.
// A condition describes the way a variant influences human health.
Conditions []*VariantAnnotation_ClinicalCondition `protobuf:"bytes,6,rep,name=conditions,proto3" json:"conditions,omitempty"`
// Describes the clinical significance of a variant.
// It is adapted from the ClinVar controlled vocabulary for clinical
// significance described at:
// http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
ClinicalSignificance VariantAnnotation_ClinicalSignificance `protobuf:"varint,7,opt,name=clinical_significance,json=clinicalSignificance,proto3,enum=google.genomics.v1.VariantAnnotation_ClinicalSignificance" json:"clinical_significance,omitempty"`
// contains filtered or unexported fields
}
func (*VariantAnnotation) Descriptor() ([]byte, []int)
Deprecated: Use VariantAnnotation.ProtoReflect.Descriptor instead.
func (x *VariantAnnotation) GetAlternateBases() string
func (x *VariantAnnotation) GetClinicalSignificance() VariantAnnotation_ClinicalSignificance
func (x *VariantAnnotation) GetConditions() []*VariantAnnotation_ClinicalCondition
func (x *VariantAnnotation) GetEffect() VariantAnnotation_Effect
func (x *VariantAnnotation) GetGeneId() string
func (x *VariantAnnotation) GetTranscriptIds() []string
func (x *VariantAnnotation) GetType() VariantAnnotation_Type
func (*VariantAnnotation) ProtoMessage()
func (x *VariantAnnotation) ProtoReflect() protoreflect.Message
func (x *VariantAnnotation) Reset()
func (x *VariantAnnotation) String() string
type VariantAnnotation_ClinicalCondition struct {
// A set of names for the condition.
Names []string `protobuf:"bytes,1,rep,name=names,proto3" json:"names,omitempty"`
// The set of external IDs for this condition.
ExternalIds []*ExternalId `protobuf:"bytes,2,rep,name=external_ids,json=externalIds,proto3" json:"external_ids,omitempty"`
// The MedGen concept id associated with this gene.
// Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
ConceptId string `protobuf:"bytes,3,opt,name=concept_id,json=conceptId,proto3" json:"concept_id,omitempty"`
// The OMIM id for this condition.
// Search for these IDs at http://omim.org/
OmimId string `protobuf:"bytes,4,opt,name=omim_id,json=omimId,proto3" json:"omim_id,omitempty"`
// contains filtered or unexported fields
}
func (*VariantAnnotation_ClinicalCondition) Descriptor() ([]byte, []int)
Deprecated: Use VariantAnnotation_ClinicalCondition.ProtoReflect.Descriptor instead.
func (x *VariantAnnotation_ClinicalCondition) GetConceptId() string
func (x *VariantAnnotation_ClinicalCondition) GetExternalIds() []*ExternalId
func (x *VariantAnnotation_ClinicalCondition) GetNames() []string
func (x *VariantAnnotation_ClinicalCondition) GetOmimId() string
func (*VariantAnnotation_ClinicalCondition) ProtoMessage()
func (x *VariantAnnotation_ClinicalCondition) ProtoReflect() protoreflect.Message
func (x *VariantAnnotation_ClinicalCondition) Reset()
func (x *VariantAnnotation_ClinicalCondition) String() string
type VariantAnnotation_ClinicalSignificance int32
const (
VariantAnnotation_CLINICAL_SIGNIFICANCE_UNSPECIFIED VariantAnnotation_ClinicalSignificance = 0
// `OTHER` should be used when no other clinical significance
// value will suffice.
VariantAnnotation_CLINICAL_SIGNIFICANCE_OTHER VariantAnnotation_ClinicalSignificance = 1
VariantAnnotation_UNCERTAIN VariantAnnotation_ClinicalSignificance = 2
VariantAnnotation_BENIGN VariantAnnotation_ClinicalSignificance = 3
VariantAnnotation_LIKELY_BENIGN VariantAnnotation_ClinicalSignificance = 4
VariantAnnotation_LIKELY_PATHOGENIC VariantAnnotation_ClinicalSignificance = 5
VariantAnnotation_PATHOGENIC VariantAnnotation_ClinicalSignificance = 6
VariantAnnotation_DRUG_RESPONSE VariantAnnotation_ClinicalSignificance = 7
VariantAnnotation_HISTOCOMPATIBILITY VariantAnnotation_ClinicalSignificance = 8
VariantAnnotation_CONFERS_SENSITIVITY VariantAnnotation_ClinicalSignificance = 9
VariantAnnotation_RISK_FACTOR VariantAnnotation_ClinicalSignificance = 10
VariantAnnotation_ASSOCIATION VariantAnnotation_ClinicalSignificance = 11
VariantAnnotation_PROTECTIVE VariantAnnotation_ClinicalSignificance = 12
// `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.
VariantAnnotation_MULTIPLE_REPORTED VariantAnnotation_ClinicalSignificance = 13
)
func (VariantAnnotation_ClinicalSignificance) Descriptor() protoreflect.EnumDescriptor
func (x VariantAnnotation_ClinicalSignificance) Enum() *VariantAnnotation_ClinicalSignificance
func (VariantAnnotation_ClinicalSignificance) EnumDescriptor() ([]byte, []int)
Deprecated: Use VariantAnnotation_ClinicalSignificance.Descriptor instead.
func (x VariantAnnotation_ClinicalSignificance) Number() protoreflect.EnumNumber
func (x VariantAnnotation_ClinicalSignificance) String() string
func (VariantAnnotation_ClinicalSignificance) Type() protoreflect.EnumType
type VariantAnnotation_Effect int32
const (
VariantAnnotation_EFFECT_UNSPECIFIED VariantAnnotation_Effect = 0
// `EFFECT_OTHER` should be used when no other Effect
// will suffice.
VariantAnnotation_EFFECT_OTHER VariantAnnotation_Effect = 1
// `FRAMESHIFT` indicates a mutation in which the insertion or
// deletion of nucleotides resulted in a frameshift change.
VariantAnnotation_FRAMESHIFT VariantAnnotation_Effect = 2
// `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.
VariantAnnotation_FRAME_PRESERVING_INDEL VariantAnnotation_Effect = 3
// `SYNONYMOUS_SNP` indicates a single nucleotide polymorphism
// mutation that results in no amino acid change.
VariantAnnotation_SYNONYMOUS_SNP VariantAnnotation_Effect = 4
// `NONSYNONYMOUS_SNP` indicates a single nucleotide
// polymorphism mutation that results in an amino acid change.
VariantAnnotation_NONSYNONYMOUS_SNP VariantAnnotation_Effect = 5
// `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`.
VariantAnnotation_STOP_GAIN VariantAnnotation_Effect = 6
// `STOP_LOSS` indicates a mutation that eliminates a
// stop codon at the variant site.
VariantAnnotation_STOP_LOSS VariantAnnotation_Effect = 7
// `SPLICE_SITE_DISRUPTION` indicates that this variant is
// found in a splice site for the associated transcript, and alters the
// normal splicing pattern.
VariantAnnotation_SPLICE_SITE_DISRUPTION VariantAnnotation_Effect = 8
)
func (VariantAnnotation_Effect) Descriptor() protoreflect.EnumDescriptor
func (x VariantAnnotation_Effect) Enum() *VariantAnnotation_Effect
func (VariantAnnotation_Effect) EnumDescriptor() ([]byte, []int)
Deprecated: Use VariantAnnotation_Effect.Descriptor instead.
func (x VariantAnnotation_Effect) Number() protoreflect.EnumNumber
func (x VariantAnnotation_Effect) String() string
func (VariantAnnotation_Effect) Type() protoreflect.EnumType
type VariantAnnotation_Type int32
const (
VariantAnnotation_TYPE_UNSPECIFIED VariantAnnotation_Type = 0
// `TYPE_OTHER` should be used when no other Type will suffice.
// Further explanation of the variant type may be included in the
// [info][google.genomics.v1.Annotation.info] field.
VariantAnnotation_TYPE_OTHER VariantAnnotation_Type = 1
// `INSERTION` indicates an insertion.
VariantAnnotation_INSERTION VariantAnnotation_Type = 2
// `DELETION` indicates a deletion.
VariantAnnotation_DELETION VariantAnnotation_Type = 3
// `SUBSTITUTION` indicates a block substitution of
// two or more nucleotides.
VariantAnnotation_SUBSTITUTION VariantAnnotation_Type = 4
// `SNP` indicates a single nucleotide polymorphism.
VariantAnnotation_SNP VariantAnnotation_Type = 5
// `STRUCTURAL` indicates a large structural variant,
// including chromosomal fusions, inversions, etc.
VariantAnnotation_STRUCTURAL VariantAnnotation_Type = 6
// `CNV` indicates a variation in copy number.
VariantAnnotation_CNV VariantAnnotation_Type = 7
)
func (VariantAnnotation_Type) Descriptor() protoreflect.EnumDescriptor
func (x VariantAnnotation_Type) Enum() *VariantAnnotation_Type
func (VariantAnnotation_Type) EnumDescriptor() ([]byte, []int)
Deprecated: Use VariantAnnotation_Type.Descriptor instead.
func (x VariantAnnotation_Type) Number() protoreflect.EnumNumber
func (x VariantAnnotation_Type) String() string
func (VariantAnnotation_Type) Type() protoreflect.EnumType
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 {
// The ID of the call set this variant call belongs to.
CallSetId string `protobuf:"bytes,8,opt,name=call_set_id,json=callSetId,proto3" json:"call_set_id,omitempty"`
// The name of the call set this variant call belongs to.
CallSetName string `protobuf:"bytes,9,opt,name=call_set_name,json=callSetName,proto3" json:"call_set_name,omitempty"`
// 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 []int32 `protobuf:"varint,7,rep,packed,name=genotype,proto3" json:"genotype,omitempty"`
// 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 `protobuf:"bytes,5,opt,name=phaseset,proto3" json:"phaseset,omitempty"`
// 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 `protobuf:"fixed64,6,rep,packed,name=genotype_likelihood,json=genotypeLikelihood,proto3" json:"genotype_likelihood,omitempty"`
// 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]*structpb.ListValue `protobuf:"bytes,2,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*VariantCall) Descriptor() ([]byte, []int)
Deprecated: Use VariantCall.ProtoReflect.Descriptor instead.
func (x *VariantCall) GetCallSetId() string
func (x *VariantCall) GetCallSetName() string
func (x *VariantCall) GetGenotype() []int32
func (x *VariantCall) GetGenotypeLikelihood() []float64
func (x *VariantCall) GetInfo() map[string]*structpb.ListValue
func (x *VariantCall) GetPhaseset() string
func (*VariantCall) ProtoMessage()
func (x *VariantCall) ProtoReflect() protoreflect.Message
func (x *VariantCall) Reset()
func (x *VariantCall) String() string
VariantServiceV1Client is the client API for VariantServiceV1 service.
For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.
type VariantServiceV1Client interface {
// Creates variant data by asynchronously importing the provided information.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// The variants for import will be merged with any existing variant that
// matches its reference sequence, start, end, reference bases, and
// alternative bases. If no such variant exists, a new one will be created.
//
// When variants are merged, the call information from the new variant
// is added to the existing variant, and Variant info fields are merged
// as specified in
// [infoMergeConfig][google.genomics.v1.ImportVariantsRequest.info_merge_config].
// 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.
ImportVariants(ctx context.Context, in *ImportVariantsRequest, opts ...grpc.CallOption) (*longrunningpb.Operation, error)
// Creates a new variant set.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// The provided variant set must have a valid `datasetId` set - all other
// fields are optional. Note that the `id` field will be ignored, as this is
// assigned by the server.
CreateVariantSet(ctx context.Context, in *CreateVariantSetRequest, opts ...grpc.CallOption) (*VariantSet, error)
// Exports variant set data to an external destination.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
ExportVariantSet(ctx context.Context, in *ExportVariantSetRequest, opts ...grpc.CallOption) (*longrunningpb.Operation, error)
// Gets a variant set by ID.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetVariantSet(ctx context.Context, in *GetVariantSetRequest, opts ...grpc.CallOption) (*VariantSet, error)
// Returns a list of all variant sets matching search criteria.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
SearchVariantSets(ctx context.Context, in *SearchVariantSetsRequest, opts ...grpc.CallOption) (*SearchVariantSetsResponse, error)
// Deletes a variant set including all variants, call sets, and calls within.
// This is not reversible.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteVariantSet(ctx context.Context, in *DeleteVariantSetRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// Updates a variant set using patch semantics.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
UpdateVariantSet(ctx context.Context, in *UpdateVariantSetRequest, opts ...grpc.CallOption) (*VariantSet, error)
// Gets a list of variants matching the criteria.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
SearchVariants(ctx context.Context, in *SearchVariantsRequest, opts ...grpc.CallOption) (*SearchVariantsResponse, error)
// Creates a new variant.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateVariant(ctx context.Context, in *CreateVariantRequest, opts ...grpc.CallOption) (*Variant, error)
// Updates a variant.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics. Returns the modified variant without
// its calls.
UpdateVariant(ctx context.Context, in *UpdateVariantRequest, opts ...grpc.CallOption) (*Variant, error)
// Deletes a variant.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteVariant(ctx context.Context, in *DeleteVariantRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// Gets a variant by ID.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetVariant(ctx context.Context, in *GetVariantRequest, opts ...grpc.CallOption) (*Variant, error)
// Merges the given variants with existing variants.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Each variant will be
// merged with an existing variant that matches its reference sequence,
// start, end, reference bases, and alternative bases. If no such variant
// exists, a new one will be created.
//
// When variants are merged, the call information from the new variant
// is added to the existing variant. Variant info fields are merged as
// specified in the
// [infoMergeConfig][google.genomics.v1.MergeVariantsRequest.info_merge_config]
// 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.
MergeVariants(ctx context.Context, in *MergeVariantsRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// Gets a list of call sets matching the criteria.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
SearchCallSets(ctx context.Context, in *SearchCallSetsRequest, opts ...grpc.CallOption) (*SearchCallSetsResponse, error)
// Creates a new call set.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateCallSet(ctx context.Context, in *CreateCallSetRequest, opts ...grpc.CallOption) (*CallSet, error)
// Updates a call set.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateCallSet(ctx context.Context, in *UpdateCallSetRequest, opts ...grpc.CallOption) (*CallSet, error)
// Deletes a call set.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteCallSet(ctx context.Context, in *DeleteCallSetRequest, opts ...grpc.CallOption) (*emptypb.Empty, error)
// Gets a call set by ID.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetCallSet(ctx context.Context, in *GetCallSetRequest, opts ...grpc.CallOption) (*CallSet, error)
}
func NewVariantServiceV1Client(cc grpc.ClientConnInterface) VariantServiceV1Client
VariantServiceV1Server is the server API for VariantServiceV1 service.
type VariantServiceV1Server interface {
// Creates variant data by asynchronously importing the provided information.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// The variants for import will be merged with any existing variant that
// matches its reference sequence, start, end, reference bases, and
// alternative bases. If no such variant exists, a new one will be created.
//
// When variants are merged, the call information from the new variant
// is added to the existing variant, and Variant info fields are merged
// as specified in
// [infoMergeConfig][google.genomics.v1.ImportVariantsRequest.info_merge_config].
// 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.
ImportVariants(context.Context, *ImportVariantsRequest) (*longrunningpb.Operation, error)
// Creates a new variant set.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// The provided variant set must have a valid `datasetId` set - all other
// fields are optional. Note that the `id` field will be ignored, as this is
// assigned by the server.
CreateVariantSet(context.Context, *CreateVariantSetRequest) (*VariantSet, error)
// Exports variant set data to an external destination.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
ExportVariantSet(context.Context, *ExportVariantSetRequest) (*longrunningpb.Operation, error)
// Gets a variant set by ID.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetVariantSet(context.Context, *GetVariantSetRequest) (*VariantSet, error)
// Returns a list of all variant sets matching search criteria.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
SearchVariantSets(context.Context, *SearchVariantSetsRequest) (*SearchVariantSetsResponse, error)
// Deletes a variant set including all variants, call sets, and calls within.
// This is not reversible.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteVariantSet(context.Context, *DeleteVariantSetRequest) (*emptypb.Empty, error)
// Updates a variant set using patch semantics.
//
// For the definitions of variant sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
UpdateVariantSet(context.Context, *UpdateVariantSetRequest) (*VariantSet, error)
// Gets a list of variants matching the criteria.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
SearchVariants(context.Context, *SearchVariantsRequest) (*SearchVariantsResponse, error)
// Creates a new variant.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateVariant(context.Context, *CreateVariantRequest) (*Variant, error)
// Updates a variant.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics. Returns the modified variant without
// its calls.
UpdateVariant(context.Context, *UpdateVariantRequest) (*Variant, error)
// Deletes a variant.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteVariant(context.Context, *DeleteVariantRequest) (*emptypb.Empty, error)
// Gets a variant by ID.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetVariant(context.Context, *GetVariantRequest) (*Variant, error)
// Merges the given variants with existing variants.
//
// For the definitions of variants and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Each variant will be
// merged with an existing variant that matches its reference sequence,
// start, end, reference bases, and alternative bases. If no such variant
// exists, a new one will be created.
//
// When variants are merged, the call information from the new variant
// is added to the existing variant. Variant info fields are merged as
// specified in the
// [infoMergeConfig][google.genomics.v1.MergeVariantsRequest.info_merge_config]
// 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.
MergeVariants(context.Context, *MergeVariantsRequest) (*emptypb.Empty, error)
// Gets a list of call sets matching the criteria.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
SearchCallSets(context.Context, *SearchCallSetsRequest) (*SearchCallSetsResponse, error)
// Creates a new call set.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
CreateCallSet(context.Context, *CreateCallSetRequest) (*CallSet, error)
// Updates a call set.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
UpdateCallSet(context.Context, *UpdateCallSetRequest) (*CallSet, error)
// Deletes a call set.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
DeleteCallSet(context.Context, *DeleteCallSetRequest) (*emptypb.Empty, error)
// Gets a call set by ID.
//
// For the definitions of call sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
GetCallSet(context.Context, *GetCallSetRequest) (*CallSet, error)
}
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-google-genomics)
type VariantSet struct {
// The dataset to which this variant set belongs.
DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"`
// The server-generated variant set ID, unique across all variant sets.
Id string `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
// 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 `protobuf:"bytes,6,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"`
// A list of all references used by the variants in a variant set
// with associated coordinate upper bounds for each one.
ReferenceBounds []*ReferenceBound `protobuf:"bytes,5,rep,name=reference_bounds,json=referenceBounds,proto3" json:"reference_bounds,omitempty"`
// The metadata associated with this variant set.
Metadata []*VariantSetMetadata `protobuf:"bytes,4,rep,name=metadata,proto3" json:"metadata,omitempty"`
// User-specified, mutable name.
Name string `protobuf:"bytes,7,opt,name=name,proto3" json:"name,omitempty"`
// A textual description of this variant set.
Description string `protobuf:"bytes,8,opt,name=description,proto3" json:"description,omitempty"`
// contains filtered or unexported fields
}
func (*VariantSet) Descriptor() ([]byte, []int)
Deprecated: Use VariantSet.ProtoReflect.Descriptor instead.
func (x *VariantSet) GetDatasetId() string
func (x *VariantSet) GetDescription() string
func (x *VariantSet) GetId() string
func (x *VariantSet) GetMetadata() []*VariantSetMetadata
func (x *VariantSet) GetName() string
func (x *VariantSet) GetReferenceBounds() []*ReferenceBound
func (x *VariantSet) GetReferenceSetId() string
func (*VariantSet) ProtoMessage()
func (x *VariantSet) ProtoReflect() protoreflect.Message
func (x *VariantSet) Reset()
func (x *VariantSet) String() string
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 {
// The top-level key.
Key string `protobuf:"bytes,1,opt,name=key,proto3" json:"key,omitempty"`
// The value field for simple metadata
Value string `protobuf:"bytes,2,opt,name=value,proto3" json:"value,omitempty"`
// 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 `protobuf:"bytes,4,opt,name=id,proto3" json:"id,omitempty"`
// The type of data. Possible types include: Integer, Float,
// Flag, Character, and String.
Type VariantSetMetadata_Type `protobuf:"varint,5,opt,name=type,proto3,enum=google.genomics.v1.VariantSetMetadata_Type" json:"type,omitempty"`
// The number of values that can be included in a field described by this
// metadata.
Number string `protobuf:"bytes,8,opt,name=number,proto3" json:"number,omitempty"`
// A textual description of this metadata.
Description string `protobuf:"bytes,7,opt,name=description,proto3" json:"description,omitempty"`
// 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]*structpb.ListValue `protobuf:"bytes,3,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
// contains filtered or unexported fields
}
func (*VariantSetMetadata) Descriptor() ([]byte, []int)
Deprecated: Use VariantSetMetadata.ProtoReflect.Descriptor instead.
func (x *VariantSetMetadata) GetDescription() string
func (x *VariantSetMetadata) GetId() string
func (x *VariantSetMetadata) GetInfo() map[string]*structpb.ListValue
func (x *VariantSetMetadata) GetKey() string
func (x *VariantSetMetadata) GetNumber() string
func (x *VariantSetMetadata) GetType() VariantSetMetadata_Type
func (x *VariantSetMetadata) GetValue() string
func (*VariantSetMetadata) ProtoMessage()
func (x *VariantSetMetadata) ProtoReflect() protoreflect.Message
func (x *VariantSetMetadata) Reset()
func (x *VariantSetMetadata) String() string
type VariantSetMetadata_Type int32
const (
VariantSetMetadata_TYPE_UNSPECIFIED VariantSetMetadata_Type = 0
VariantSetMetadata_INTEGER VariantSetMetadata_Type = 1
VariantSetMetadata_FLOAT VariantSetMetadata_Type = 2
VariantSetMetadata_FLAG VariantSetMetadata_Type = 3
VariantSetMetadata_CHARACTER VariantSetMetadata_Type = 4
VariantSetMetadata_STRING VariantSetMetadata_Type = 5
)
func (VariantSetMetadata_Type) Descriptor() protoreflect.EnumDescriptor
func (x VariantSetMetadata_Type) Enum() *VariantSetMetadata_Type
func (VariantSetMetadata_Type) EnumDescriptor() ([]byte, []int)
Deprecated: Use VariantSetMetadata_Type.Descriptor instead.
func (x VariantSetMetadata_Type) Number() protoreflect.EnumNumber
func (x VariantSetMetadata_Type) String() string
func (VariantSetMetadata_Type) Type() protoreflect.EnumType