import "google.golang.org/genproto/googleapis/genomics/v1"
annotations.pb.go cigar.pb.go datasets.pb.go operations.pb.go position.pb.go range.pb.go readalignment.pb.go readgroup.pb.go readgroupset.pb.go reads.pb.go references.pb.go variants.pb.go
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 AnnotationType.
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_Type.
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_Effect.
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 VariantAnnotation_ClinicalSignificance.
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 CigarUnit_Operation.
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 ImportReadGroupSetsRequest_PartitionStrategy.
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 InfoMergeOperation.
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 VariantSetMetadata_Type.
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 ImportVariantsRequest_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, } )
Enum value maps for ExportVariantSetRequest_Format.
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)
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 }
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`.
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
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) }
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.
func NewAnnotationServiceV1Client(cc grpc.ClientConnInterface) AnnotationServiceV1Client
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) }
AnnotationServiceV1Server is the server API for AnnotationServiceV1 service.
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 }
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'.
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`.
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
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 }
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)
Deprecated: Use CallSet.ProtoReflect.Descriptor instead.
func (x *CallSet) ProtoReflect() protoreflect.Message
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 }
A single CIGAR operation.
Deprecated: Use CigarUnit.ProtoReflect.Descriptor instead.
func (x *CigarUnit) GetOperation() CigarUnit_Operation
func (x *CigarUnit) ProtoReflect() protoreflect.Message
Describes the different types of CIGAR alignment operations that exist. Used wherever CIGAR alignments are used.
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
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 }
A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.
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
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 }
The CreateVariantSet request
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
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 }
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)
Deprecated: Use Dataset.ProtoReflect.Descriptor instead.
func (x *Dataset) GetCreateTime() *timestamppb.Timestamp
func (x *Dataset) ProtoReflect() protoreflect.Message
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 *v1.SetIamPolicyRequest, opts ...grpc.CallOption) (*v1.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 *v1.GetIamPolicyRequest, opts ...grpc.CallOption) (*v1.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 *v1.TestIamPermissionsRequest, opts ...grpc.CallOption) (*v1.TestIamPermissionsResponse, error) }
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.
func NewDatasetServiceV1Client(cc grpc.ClientConnInterface) DatasetServiceV1Client
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, *v1.SetIamPolicyRequest) (*v1.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, *v1.GetIamPolicyRequest) (*v1.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, *v1.TestIamPermissionsRequest) (*v1.TestIamPermissionsResponse, error) }
DatasetServiceV1Server is the server API for DatasetServiceV1 service.
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
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 }
The delete variant set request.
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
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 }
The read group set export request.
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
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 }
The variant data export request.
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
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
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 }
The variant set request.
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
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 }
The read group set import request.
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
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
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 }
The read group set import response.
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
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 }
The variant data import request.
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
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
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 }
The variant data import response.
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.
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
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 }
A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.
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
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 }
The dataset list request.
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
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 }
The dataset list response.
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
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 }
An event that occurred during an [Operation][google.longrunning.Operation].
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
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 }
Metadata describing an [Operation][google.longrunning.Operation].
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
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 }
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.
Deprecated: Use Position.ProtoReflect.Descriptor instead.
func (x *Position) ProtoReflect() protoreflect.Message
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 }
A 0-based half-open genomic coordinate range for search requests.
Deprecated: Use Range.ProtoReflect.Descriptor instead.
func (x *Range) ProtoReflect() protoreflect.Message
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 }
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
Deprecated: Use Read.ProtoReflect.Descriptor instead.
func (x *Read) GetAlignment() *LinearAlignment
func (x *Read) ProtoReflect() protoreflect.Message
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 }
A read group is all the data that's processed the same way by the sequencer.
Deprecated: Use ReadGroup.ProtoReflect.Descriptor instead.
func (x *ReadGroup) GetExperiment() *ReadGroup_Experiment
func (x *ReadGroup) GetPrograms() []*ReadGroup_Program
func (x *ReadGroup) ProtoReflect() protoreflect.Message
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 }
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)
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
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) (*longrunning.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) (*longrunning.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) }
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.
func NewReadServiceV1Client(cc grpc.ClientConnInterface) ReadServiceV1Client
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) (*longrunning.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) (*longrunning.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) }
ReadServiceV1Server is the server API for ReadServiceV1 service.
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 }
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)
Deprecated: Use Reference.ProtoReflect.Descriptor instead.
func (x *Reference) ProtoReflect() protoreflect.Message
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 }
ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
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
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) }
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.
func NewReferenceServiceV1Client(cc grpc.ClientConnInterface) ReferenceServiceV1Client
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) }
ReferenceServiceV1Server is the server API for ReferenceServiceV1 service.
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 }
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)
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
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 }
The call set search request.
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
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 }
The call set search response.
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
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 }
The read group set search request.
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
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 }
The read group set search response.
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
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 }
The read search request.
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
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 }
The read search response.
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
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 }
The search variant sets request.
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
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 }
The search variant sets response.
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
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 }
The variant search request.
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
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 }
The variant search response.
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
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 }
The stream reads request.
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