| // Copyright 2016 Google Inc. |
| // |
| // Licensed under the Apache License, Version 2.0 (the "License"); |
| // you may not use this file except in compliance with the License. |
| // You may obtain a copy of the License at |
| // |
| // http://www.apache.org/licenses/LICENSE-2.0 |
| // |
| // Unless required by applicable law or agreed to in writing, software |
| // distributed under the License is distributed on an "AS IS" BASIS, |
| // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
| // See the License for the specific language governing permissions and |
| // limitations under the License. |
| |
| // Code generated by protoc-gen-go. DO NOT EDIT. |
| // versions: |
| // protoc-gen-go v1.22.0 |
| // protoc v3.12.2 |
| // source: google/genomics/v1/reads.proto |
| |
| package genomics |
| |
| import ( |
| context "context" |
| reflect "reflect" |
| sync "sync" |
| |
| proto "github.com/golang/protobuf/proto" |
| empty "github.com/golang/protobuf/ptypes/empty" |
| _ "google.golang.org/genproto/googleapis/api/annotations" |
| longrunning "google.golang.org/genproto/googleapis/longrunning" |
| field_mask "google.golang.org/genproto/protobuf/field_mask" |
| grpc "google.golang.org/grpc" |
| codes "google.golang.org/grpc/codes" |
| status "google.golang.org/grpc/status" |
| protoreflect "google.golang.org/protobuf/reflect/protoreflect" |
| protoimpl "google.golang.org/protobuf/runtime/protoimpl" |
| ) |
| |
| const ( |
| // Verify that this generated code is sufficiently up-to-date. |
| _ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion) |
| // Verify that runtime/protoimpl is sufficiently up-to-date. |
| _ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20) |
| ) |
| |
| // This is a compile-time assertion that a sufficiently up-to-date version |
| // of the legacy proto package is being used. |
| const _ = proto.ProtoPackageIsVersion4 |
| |
| type ImportReadGroupSetsRequest_PartitionStrategy int32 |
| |
| const ( |
| ImportReadGroupSetsRequest_PARTITION_STRATEGY_UNSPECIFIED ImportReadGroupSetsRequest_PartitionStrategy = 0 |
| // In most cases, this strategy yields one read group set per file. This is |
| // the default behavior. |
| // |
| // Allocate one read group set per file per sample. For BAM files, read |
| // groups are considered to share a sample if they have identical sample |
| // names. Furthermore, all reads for each file which do not belong to a read |
| // group, if any, will be grouped into a single read group set per-file. |
| ImportReadGroupSetsRequest_PER_FILE_PER_SAMPLE ImportReadGroupSetsRequest_PartitionStrategy = 1 |
| // Includes all read groups in all imported files into a single read group |
| // set. Requires that the headers for all imported files are equivalent. All |
| // reads which do not belong to a read group, if any, will be grouped into a |
| // separate read group set. |
| ImportReadGroupSetsRequest_MERGE_ALL ImportReadGroupSetsRequest_PartitionStrategy = 2 |
| ) |
| |
| // Enum value maps for ImportReadGroupSetsRequest_PartitionStrategy. |
| var ( |
| ImportReadGroupSetsRequest_PartitionStrategy_name = map[int32]string{ |
| 0: "PARTITION_STRATEGY_UNSPECIFIED", |
| 1: "PER_FILE_PER_SAMPLE", |
| 2: "MERGE_ALL", |
| } |
| ImportReadGroupSetsRequest_PartitionStrategy_value = map[string]int32{ |
| "PARTITION_STRATEGY_UNSPECIFIED": 0, |
| "PER_FILE_PER_SAMPLE": 1, |
| "MERGE_ALL": 2, |
| } |
| ) |
| |
| func (x ImportReadGroupSetsRequest_PartitionStrategy) Enum() *ImportReadGroupSetsRequest_PartitionStrategy { |
| p := new(ImportReadGroupSetsRequest_PartitionStrategy) |
| *p = x |
| return p |
| } |
| |
| func (x ImportReadGroupSetsRequest_PartitionStrategy) String() string { |
| return protoimpl.X.EnumStringOf(x.Descriptor(), protoreflect.EnumNumber(x)) |
| } |
| |
| func (ImportReadGroupSetsRequest_PartitionStrategy) Descriptor() protoreflect.EnumDescriptor { |
| return file_google_genomics_v1_reads_proto_enumTypes[0].Descriptor() |
| } |
| |
| func (ImportReadGroupSetsRequest_PartitionStrategy) Type() protoreflect.EnumType { |
| return &file_google_genomics_v1_reads_proto_enumTypes[0] |
| } |
| |
| func (x ImportReadGroupSetsRequest_PartitionStrategy) Number() protoreflect.EnumNumber { |
| return protoreflect.EnumNumber(x) |
| } |
| |
| // Deprecated: Use ImportReadGroupSetsRequest_PartitionStrategy.Descriptor instead. |
| func (ImportReadGroupSetsRequest_PartitionStrategy) EnumDescriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{2, 0} |
| } |
| |
| // The read group set search request. |
| type SearchReadGroupSetsRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *SearchReadGroupSetsRequest) Reset() { |
| *x = SearchReadGroupSetsRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[0] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *SearchReadGroupSetsRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*SearchReadGroupSetsRequest) ProtoMessage() {} |
| |
| func (x *SearchReadGroupSetsRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[0] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use SearchReadGroupSetsRequest.ProtoReflect.Descriptor instead. |
| func (*SearchReadGroupSetsRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{0} |
| } |
| |
| func (x *SearchReadGroupSetsRequest) GetDatasetIds() []string { |
| if x != nil { |
| return x.DatasetIds |
| } |
| return nil |
| } |
| |
| func (x *SearchReadGroupSetsRequest) GetName() string { |
| if x != nil { |
| return x.Name |
| } |
| return "" |
| } |
| |
| func (x *SearchReadGroupSetsRequest) GetPageToken() string { |
| if x != nil { |
| return x.PageToken |
| } |
| return "" |
| } |
| |
| func (x *SearchReadGroupSetsRequest) GetPageSize() int32 { |
| if x != nil { |
| return x.PageSize |
| } |
| return 0 |
| } |
| |
| // The read group set search response. |
| type SearchReadGroupSetsResponse struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *SearchReadGroupSetsResponse) Reset() { |
| *x = SearchReadGroupSetsResponse{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[1] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *SearchReadGroupSetsResponse) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*SearchReadGroupSetsResponse) ProtoMessage() {} |
| |
| func (x *SearchReadGroupSetsResponse) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[1] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use SearchReadGroupSetsResponse.ProtoReflect.Descriptor instead. |
| func (*SearchReadGroupSetsResponse) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{1} |
| } |
| |
| func (x *SearchReadGroupSetsResponse) GetReadGroupSets() []*ReadGroupSet { |
| if x != nil { |
| return x.ReadGroupSets |
| } |
| return nil |
| } |
| |
| func (x *SearchReadGroupSetsResponse) GetNextPageToken() string { |
| if x != nil { |
| return x.NextPageToken |
| } |
| return "" |
| } |
| |
| // The read group set import request. |
| type ImportReadGroupSetsRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *ImportReadGroupSetsRequest) Reset() { |
| *x = ImportReadGroupSetsRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[2] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *ImportReadGroupSetsRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*ImportReadGroupSetsRequest) ProtoMessage() {} |
| |
| func (x *ImportReadGroupSetsRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[2] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use ImportReadGroupSetsRequest.ProtoReflect.Descriptor instead. |
| func (*ImportReadGroupSetsRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{2} |
| } |
| |
| func (x *ImportReadGroupSetsRequest) GetDatasetId() string { |
| if x != nil { |
| return x.DatasetId |
| } |
| return "" |
| } |
| |
| func (x *ImportReadGroupSetsRequest) GetReferenceSetId() string { |
| if x != nil { |
| return x.ReferenceSetId |
| } |
| return "" |
| } |
| |
| func (x *ImportReadGroupSetsRequest) GetSourceUris() []string { |
| if x != nil { |
| return x.SourceUris |
| } |
| return nil |
| } |
| |
| func (x *ImportReadGroupSetsRequest) GetPartitionStrategy() ImportReadGroupSetsRequest_PartitionStrategy { |
| if x != nil { |
| return x.PartitionStrategy |
| } |
| return ImportReadGroupSetsRequest_PARTITION_STRATEGY_UNSPECIFIED |
| } |
| |
| // The read group set import response. |
| type ImportReadGroupSetsResponse struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *ImportReadGroupSetsResponse) Reset() { |
| *x = ImportReadGroupSetsResponse{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[3] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *ImportReadGroupSetsResponse) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*ImportReadGroupSetsResponse) ProtoMessage() {} |
| |
| func (x *ImportReadGroupSetsResponse) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[3] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use ImportReadGroupSetsResponse.ProtoReflect.Descriptor instead. |
| func (*ImportReadGroupSetsResponse) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{3} |
| } |
| |
| func (x *ImportReadGroupSetsResponse) GetReadGroupSetIds() []string { |
| if x != nil { |
| return x.ReadGroupSetIds |
| } |
| return nil |
| } |
| |
| // The read group set export request. |
| type ExportReadGroupSetRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *ExportReadGroupSetRequest) Reset() { |
| *x = ExportReadGroupSetRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[4] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *ExportReadGroupSetRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*ExportReadGroupSetRequest) ProtoMessage() {} |
| |
| func (x *ExportReadGroupSetRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[4] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use ExportReadGroupSetRequest.ProtoReflect.Descriptor instead. |
| func (*ExportReadGroupSetRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{4} |
| } |
| |
| func (x *ExportReadGroupSetRequest) GetProjectId() string { |
| if x != nil { |
| return x.ProjectId |
| } |
| return "" |
| } |
| |
| func (x *ExportReadGroupSetRequest) GetExportUri() string { |
| if x != nil { |
| return x.ExportUri |
| } |
| return "" |
| } |
| |
| func (x *ExportReadGroupSetRequest) GetReadGroupSetId() string { |
| if x != nil { |
| return x.ReadGroupSetId |
| } |
| return "" |
| } |
| |
| func (x *ExportReadGroupSetRequest) GetReferenceNames() []string { |
| if x != nil { |
| return x.ReferenceNames |
| } |
| return nil |
| } |
| |
| type UpdateReadGroupSetRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // The ID of the read group set to be updated. The caller must have WRITE |
| // permissions to the dataset associated with this read group set. |
| ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` |
| // The new read group set data. See `updateMask` for details on mutability of |
| // fields. |
| ReadGroupSet *ReadGroupSet `protobuf:"bytes,2,opt,name=read_group_set,json=readGroupSet,proto3" json:"read_group_set,omitempty"` |
| // An optional mask specifying which fields to update. Supported fields: |
| // |
| // * [name][google.genomics.v1.ReadGroupSet.name]. |
| // * [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id]. |
| // |
| // Leaving `updateMask` unset is equivalent to specifying all mutable |
| // fields. |
| UpdateMask *field_mask.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"` |
| } |
| |
| func (x *UpdateReadGroupSetRequest) Reset() { |
| *x = UpdateReadGroupSetRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[5] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *UpdateReadGroupSetRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*UpdateReadGroupSetRequest) ProtoMessage() {} |
| |
| func (x *UpdateReadGroupSetRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[5] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use UpdateReadGroupSetRequest.ProtoReflect.Descriptor instead. |
| func (*UpdateReadGroupSetRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{5} |
| } |
| |
| func (x *UpdateReadGroupSetRequest) GetReadGroupSetId() string { |
| if x != nil { |
| return x.ReadGroupSetId |
| } |
| return "" |
| } |
| |
| func (x *UpdateReadGroupSetRequest) GetReadGroupSet() *ReadGroupSet { |
| if x != nil { |
| return x.ReadGroupSet |
| } |
| return nil |
| } |
| |
| func (x *UpdateReadGroupSetRequest) GetUpdateMask() *field_mask.FieldMask { |
| if x != nil { |
| return x.UpdateMask |
| } |
| return nil |
| } |
| |
| type DeleteReadGroupSetRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *DeleteReadGroupSetRequest) Reset() { |
| *x = DeleteReadGroupSetRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[6] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *DeleteReadGroupSetRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*DeleteReadGroupSetRequest) ProtoMessage() {} |
| |
| func (x *DeleteReadGroupSetRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[6] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use DeleteReadGroupSetRequest.ProtoReflect.Descriptor instead. |
| func (*DeleteReadGroupSetRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{6} |
| } |
| |
| func (x *DeleteReadGroupSetRequest) GetReadGroupSetId() string { |
| if x != nil { |
| return x.ReadGroupSetId |
| } |
| return "" |
| } |
| |
| type GetReadGroupSetRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *GetReadGroupSetRequest) Reset() { |
| *x = GetReadGroupSetRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[7] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *GetReadGroupSetRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*GetReadGroupSetRequest) ProtoMessage() {} |
| |
| func (x *GetReadGroupSetRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[7] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use GetReadGroupSetRequest.ProtoReflect.Descriptor instead. |
| func (*GetReadGroupSetRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{7} |
| } |
| |
| func (x *GetReadGroupSetRequest) GetReadGroupSetId() string { |
| if x != nil { |
| return x.ReadGroupSetId |
| } |
| return "" |
| } |
| |
| type ListCoverageBucketsRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *ListCoverageBucketsRequest) Reset() { |
| *x = ListCoverageBucketsRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[8] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *ListCoverageBucketsRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*ListCoverageBucketsRequest) ProtoMessage() {} |
| |
| func (x *ListCoverageBucketsRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[8] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use ListCoverageBucketsRequest.ProtoReflect.Descriptor instead. |
| func (*ListCoverageBucketsRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{8} |
| } |
| |
| func (x *ListCoverageBucketsRequest) GetReadGroupSetId() string { |
| if x != nil { |
| return x.ReadGroupSetId |
| } |
| return "" |
| } |
| |
| func (x *ListCoverageBucketsRequest) GetReferenceName() string { |
| if x != nil { |
| return x.ReferenceName |
| } |
| return "" |
| } |
| |
| func (x *ListCoverageBucketsRequest) GetStart() int64 { |
| if x != nil { |
| return x.Start |
| } |
| return 0 |
| } |
| |
| func (x *ListCoverageBucketsRequest) GetEnd() int64 { |
| if x != nil { |
| return x.End |
| } |
| return 0 |
| } |
| |
| func (x *ListCoverageBucketsRequest) GetTargetBucketWidth() int64 { |
| if x != nil { |
| return x.TargetBucketWidth |
| } |
| return 0 |
| } |
| |
| func (x *ListCoverageBucketsRequest) GetPageToken() string { |
| if x != nil { |
| return x.PageToken |
| } |
| return "" |
| } |
| |
| func (x *ListCoverageBucketsRequest) GetPageSize() int32 { |
| if x != nil { |
| return x.PageSize |
| } |
| return 0 |
| } |
| |
| // A bucket over which read coverage has been precomputed. A bucket corresponds |
| // to a specific range of the reference sequence. |
| type CoverageBucket struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *CoverageBucket) Reset() { |
| *x = CoverageBucket{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[9] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *CoverageBucket) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*CoverageBucket) ProtoMessage() {} |
| |
| func (x *CoverageBucket) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[9] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use CoverageBucket.ProtoReflect.Descriptor instead. |
| func (*CoverageBucket) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{9} |
| } |
| |
| func (x *CoverageBucket) GetRange() *Range { |
| if x != nil { |
| return x.Range |
| } |
| return nil |
| } |
| |
| func (x *CoverageBucket) GetMeanCoverage() float32 { |
| if x != nil { |
| return x.MeanCoverage |
| } |
| return 0 |
| } |
| |
| type ListCoverageBucketsResponse struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *ListCoverageBucketsResponse) Reset() { |
| *x = ListCoverageBucketsResponse{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[10] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *ListCoverageBucketsResponse) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*ListCoverageBucketsResponse) ProtoMessage() {} |
| |
| func (x *ListCoverageBucketsResponse) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[10] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use ListCoverageBucketsResponse.ProtoReflect.Descriptor instead. |
| func (*ListCoverageBucketsResponse) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{10} |
| } |
| |
| func (x *ListCoverageBucketsResponse) GetBucketWidth() int64 { |
| if x != nil { |
| return x.BucketWidth |
| } |
| return 0 |
| } |
| |
| func (x *ListCoverageBucketsResponse) GetCoverageBuckets() []*CoverageBucket { |
| if x != nil { |
| return x.CoverageBuckets |
| } |
| return nil |
| } |
| |
| func (x *ListCoverageBucketsResponse) GetNextPageToken() string { |
| if x != nil { |
| return x.NextPageToken |
| } |
| return "" |
| } |
| |
| // The read search request. |
| type SearchReadsRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *SearchReadsRequest) Reset() { |
| *x = SearchReadsRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[11] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *SearchReadsRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*SearchReadsRequest) ProtoMessage() {} |
| |
| func (x *SearchReadsRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[11] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use SearchReadsRequest.ProtoReflect.Descriptor instead. |
| func (*SearchReadsRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{11} |
| } |
| |
| func (x *SearchReadsRequest) GetReadGroupSetIds() []string { |
| if x != nil { |
| return x.ReadGroupSetIds |
| } |
| return nil |
| } |
| |
| func (x *SearchReadsRequest) GetReadGroupIds() []string { |
| if x != nil { |
| return x.ReadGroupIds |
| } |
| return nil |
| } |
| |
| func (x *SearchReadsRequest) GetReferenceName() string { |
| if x != nil { |
| return x.ReferenceName |
| } |
| return "" |
| } |
| |
| func (x *SearchReadsRequest) GetStart() int64 { |
| if x != nil { |
| return x.Start |
| } |
| return 0 |
| } |
| |
| func (x *SearchReadsRequest) GetEnd() int64 { |
| if x != nil { |
| return x.End |
| } |
| return 0 |
| } |
| |
| func (x *SearchReadsRequest) GetPageToken() string { |
| if x != nil { |
| return x.PageToken |
| } |
| return "" |
| } |
| |
| func (x *SearchReadsRequest) GetPageSize() int32 { |
| if x != nil { |
| return x.PageSize |
| } |
| return 0 |
| } |
| |
| // The read search response. |
| type SearchReadsResponse struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *SearchReadsResponse) Reset() { |
| *x = SearchReadsResponse{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[12] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *SearchReadsResponse) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*SearchReadsResponse) ProtoMessage() {} |
| |
| func (x *SearchReadsResponse) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[12] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use SearchReadsResponse.ProtoReflect.Descriptor instead. |
| func (*SearchReadsResponse) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{12} |
| } |
| |
| func (x *SearchReadsResponse) GetAlignments() []*Read { |
| if x != nil { |
| return x.Alignments |
| } |
| return nil |
| } |
| |
| func (x *SearchReadsResponse) GetNextPageToken() string { |
| if x != nil { |
| return x.NextPageToken |
| } |
| return "" |
| } |
| |
| // The stream reads request. |
| type StreamReadsRequest struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| // 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"` |
| } |
| |
| func (x *StreamReadsRequest) Reset() { |
| *x = StreamReadsRequest{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[13] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *StreamReadsRequest) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*StreamReadsRequest) ProtoMessage() {} |
| |
| func (x *StreamReadsRequest) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[13] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use StreamReadsRequest.ProtoReflect.Descriptor instead. |
| func (*StreamReadsRequest) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{13} |
| } |
| |
| func (x *StreamReadsRequest) GetProjectId() string { |
| if x != nil { |
| return x.ProjectId |
| } |
| return "" |
| } |
| |
| func (x *StreamReadsRequest) GetReadGroupSetId() string { |
| if x != nil { |
| return x.ReadGroupSetId |
| } |
| return "" |
| } |
| |
| func (x *StreamReadsRequest) GetReferenceName() string { |
| if x != nil { |
| return x.ReferenceName |
| } |
| return "" |
| } |
| |
| func (x *StreamReadsRequest) GetStart() int64 { |
| if x != nil { |
| return x.Start |
| } |
| return 0 |
| } |
| |
| func (x *StreamReadsRequest) GetEnd() int64 { |
| if x != nil { |
| return x.End |
| } |
| return 0 |
| } |
| |
| func (x *StreamReadsRequest) GetShard() int32 { |
| if x != nil { |
| return x.Shard |
| } |
| return 0 |
| } |
| |
| func (x *StreamReadsRequest) GetTotalShards() int32 { |
| if x != nil { |
| return x.TotalShards |
| } |
| return 0 |
| } |
| |
| type StreamReadsResponse struct { |
| state protoimpl.MessageState |
| sizeCache protoimpl.SizeCache |
| unknownFields protoimpl.UnknownFields |
| |
| Alignments []*Read `protobuf:"bytes,1,rep,name=alignments,proto3" json:"alignments,omitempty"` |
| } |
| |
| func (x *StreamReadsResponse) Reset() { |
| *x = StreamReadsResponse{} |
| if protoimpl.UnsafeEnabled { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[14] |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| ms.StoreMessageInfo(mi) |
| } |
| } |
| |
| func (x *StreamReadsResponse) String() string { |
| return protoimpl.X.MessageStringOf(x) |
| } |
| |
| func (*StreamReadsResponse) ProtoMessage() {} |
| |
| func (x *StreamReadsResponse) ProtoReflect() protoreflect.Message { |
| mi := &file_google_genomics_v1_reads_proto_msgTypes[14] |
| if protoimpl.UnsafeEnabled && x != nil { |
| ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) |
| if ms.LoadMessageInfo() == nil { |
| ms.StoreMessageInfo(mi) |
| } |
| return ms |
| } |
| return mi.MessageOf(x) |
| } |
| |
| // Deprecated: Use StreamReadsResponse.ProtoReflect.Descriptor instead. |
| func (*StreamReadsResponse) Descriptor() ([]byte, []int) { |
| return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{14} |
| } |
| |
| func (x *StreamReadsResponse) GetAlignments() []*Read { |
| if x != nil { |
| return x.Alignments |
| } |
| return nil |
| } |
| |
| var File_google_genomics_v1_reads_proto protoreflect.FileDescriptor |
| |
| var file_google_genomics_v1_reads_proto_rawDesc = []byte{ |
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| } |
| |
| var ( |
| file_google_genomics_v1_reads_proto_rawDescOnce sync.Once |
| file_google_genomics_v1_reads_proto_rawDescData = file_google_genomics_v1_reads_proto_rawDesc |
| ) |
| |
| func file_google_genomics_v1_reads_proto_rawDescGZIP() []byte { |
| file_google_genomics_v1_reads_proto_rawDescOnce.Do(func() { |
| file_google_genomics_v1_reads_proto_rawDescData = protoimpl.X.CompressGZIP(file_google_genomics_v1_reads_proto_rawDescData) |
| }) |
| return file_google_genomics_v1_reads_proto_rawDescData |
| } |
| |
| var file_google_genomics_v1_reads_proto_enumTypes = make([]protoimpl.EnumInfo, 1) |
| var file_google_genomics_v1_reads_proto_msgTypes = make([]protoimpl.MessageInfo, 15) |
| var file_google_genomics_v1_reads_proto_goTypes = []interface{}{ |
| (ImportReadGroupSetsRequest_PartitionStrategy)(0), // 0: google.genomics.v1.ImportReadGroupSetsRequest.PartitionStrategy |
| (*SearchReadGroupSetsRequest)(nil), // 1: google.genomics.v1.SearchReadGroupSetsRequest |
| (*SearchReadGroupSetsResponse)(nil), // 2: google.genomics.v1.SearchReadGroupSetsResponse |
| (*ImportReadGroupSetsRequest)(nil), // 3: google.genomics.v1.ImportReadGroupSetsRequest |
| (*ImportReadGroupSetsResponse)(nil), // 4: google.genomics.v1.ImportReadGroupSetsResponse |
| (*ExportReadGroupSetRequest)(nil), // 5: google.genomics.v1.ExportReadGroupSetRequest |
| (*UpdateReadGroupSetRequest)(nil), // 6: google.genomics.v1.UpdateReadGroupSetRequest |
| (*DeleteReadGroupSetRequest)(nil), // 7: google.genomics.v1.DeleteReadGroupSetRequest |
| (*GetReadGroupSetRequest)(nil), // 8: google.genomics.v1.GetReadGroupSetRequest |
| (*ListCoverageBucketsRequest)(nil), // 9: google.genomics.v1.ListCoverageBucketsRequest |
| (*CoverageBucket)(nil), // 10: google.genomics.v1.CoverageBucket |
| (*ListCoverageBucketsResponse)(nil), // 11: google.genomics.v1.ListCoverageBucketsResponse |
| (*SearchReadsRequest)(nil), // 12: google.genomics.v1.SearchReadsRequest |
| (*SearchReadsResponse)(nil), // 13: google.genomics.v1.SearchReadsResponse |
| (*StreamReadsRequest)(nil), // 14: google.genomics.v1.StreamReadsRequest |
| (*StreamReadsResponse)(nil), // 15: google.genomics.v1.StreamReadsResponse |
| (*ReadGroupSet)(nil), // 16: google.genomics.v1.ReadGroupSet |
| (*field_mask.FieldMask)(nil), // 17: google.protobuf.FieldMask |
| (*Range)(nil), // 18: google.genomics.v1.Range |
| (*Read)(nil), // 19: google.genomics.v1.Read |
| (*longrunning.Operation)(nil), // 20: google.longrunning.Operation |
| (*empty.Empty)(nil), // 21: google.protobuf.Empty |
| } |
| var file_google_genomics_v1_reads_proto_depIdxs = []int32{ |
| 16, // 0: google.genomics.v1.SearchReadGroupSetsResponse.read_group_sets:type_name -> google.genomics.v1.ReadGroupSet |
| 0, // 1: google.genomics.v1.ImportReadGroupSetsRequest.partition_strategy:type_name -> google.genomics.v1.ImportReadGroupSetsRequest.PartitionStrategy |
| 16, // 2: google.genomics.v1.UpdateReadGroupSetRequest.read_group_set:type_name -> google.genomics.v1.ReadGroupSet |
| 17, // 3: google.genomics.v1.UpdateReadGroupSetRequest.update_mask:type_name -> google.protobuf.FieldMask |
| 18, // 4: google.genomics.v1.CoverageBucket.range:type_name -> google.genomics.v1.Range |
| 10, // 5: google.genomics.v1.ListCoverageBucketsResponse.coverage_buckets:type_name -> google.genomics.v1.CoverageBucket |
| 19, // 6: google.genomics.v1.SearchReadsResponse.alignments:type_name -> google.genomics.v1.Read |
| 19, // 7: google.genomics.v1.StreamReadsResponse.alignments:type_name -> google.genomics.v1.Read |
| 14, // 8: google.genomics.v1.StreamingReadService.StreamReads:input_type -> google.genomics.v1.StreamReadsRequest |
| 3, // 9: google.genomics.v1.ReadServiceV1.ImportReadGroupSets:input_type -> google.genomics.v1.ImportReadGroupSetsRequest |
| 5, // 10: google.genomics.v1.ReadServiceV1.ExportReadGroupSet:input_type -> google.genomics.v1.ExportReadGroupSetRequest |
| 1, // 11: google.genomics.v1.ReadServiceV1.SearchReadGroupSets:input_type -> google.genomics.v1.SearchReadGroupSetsRequest |
| 6, // 12: google.genomics.v1.ReadServiceV1.UpdateReadGroupSet:input_type -> google.genomics.v1.UpdateReadGroupSetRequest |
| 7, // 13: google.genomics.v1.ReadServiceV1.DeleteReadGroupSet:input_type -> google.genomics.v1.DeleteReadGroupSetRequest |
| 8, // 14: google.genomics.v1.ReadServiceV1.GetReadGroupSet:input_type -> google.genomics.v1.GetReadGroupSetRequest |
| 9, // 15: google.genomics.v1.ReadServiceV1.ListCoverageBuckets:input_type -> google.genomics.v1.ListCoverageBucketsRequest |
| 12, // 16: google.genomics.v1.ReadServiceV1.SearchReads:input_type -> google.genomics.v1.SearchReadsRequest |
| 15, // 17: google.genomics.v1.StreamingReadService.StreamReads:output_type -> google.genomics.v1.StreamReadsResponse |
| 20, // 18: google.genomics.v1.ReadServiceV1.ImportReadGroupSets:output_type -> google.longrunning.Operation |
| 20, // 19: google.genomics.v1.ReadServiceV1.ExportReadGroupSet:output_type -> google.longrunning.Operation |
| 2, // 20: google.genomics.v1.ReadServiceV1.SearchReadGroupSets:output_type -> google.genomics.v1.SearchReadGroupSetsResponse |
| 16, // 21: google.genomics.v1.ReadServiceV1.UpdateReadGroupSet:output_type -> google.genomics.v1.ReadGroupSet |
| 21, // 22: google.genomics.v1.ReadServiceV1.DeleteReadGroupSet:output_type -> google.protobuf.Empty |
| 16, // 23: google.genomics.v1.ReadServiceV1.GetReadGroupSet:output_type -> google.genomics.v1.ReadGroupSet |
| 11, // 24: google.genomics.v1.ReadServiceV1.ListCoverageBuckets:output_type -> google.genomics.v1.ListCoverageBucketsResponse |
| 13, // 25: google.genomics.v1.ReadServiceV1.SearchReads:output_type -> google.genomics.v1.SearchReadsResponse |
| 17, // [17:26] is the sub-list for method output_type |
| 8, // [8:17] is the sub-list for method input_type |
| 8, // [8:8] is the sub-list for extension type_name |
| 8, // [8:8] is the sub-list for extension extendee |
| 0, // [0:8] is the sub-list for field type_name |
| } |
| |
| func init() { file_google_genomics_v1_reads_proto_init() } |
| func file_google_genomics_v1_reads_proto_init() { |
| if File_google_genomics_v1_reads_proto != nil { |
| return |
| } |
| file_google_genomics_v1_range_proto_init() |
| file_google_genomics_v1_readalignment_proto_init() |
| file_google_genomics_v1_readgroupset_proto_init() |
| if !protoimpl.UnsafeEnabled { |
| file_google_genomics_v1_reads_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*SearchReadGroupSetsRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[1].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*SearchReadGroupSetsResponse); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[2].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*ImportReadGroupSetsRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[3].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*ImportReadGroupSetsResponse); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[4].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*ExportReadGroupSetRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[5].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*UpdateReadGroupSetRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[6].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*DeleteReadGroupSetRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[7].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*GetReadGroupSetRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[8].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*ListCoverageBucketsRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[9].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*CoverageBucket); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[10].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*ListCoverageBucketsResponse); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[11].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*SearchReadsRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[12].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*SearchReadsResponse); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[13].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*StreamReadsRequest); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| file_google_genomics_v1_reads_proto_msgTypes[14].Exporter = func(v interface{}, i int) interface{} { |
| switch v := v.(*StreamReadsResponse); i { |
| case 0: |
| return &v.state |
| case 1: |
| return &v.sizeCache |
| case 2: |
| return &v.unknownFields |
| default: |
| return nil |
| } |
| } |
| } |
| type x struct{} |
| out := protoimpl.TypeBuilder{ |
| File: protoimpl.DescBuilder{ |
| GoPackagePath: reflect.TypeOf(x{}).PkgPath(), |
| RawDescriptor: file_google_genomics_v1_reads_proto_rawDesc, |
| NumEnums: 1, |
| NumMessages: 15, |
| NumExtensions: 0, |
| NumServices: 2, |
| }, |
| GoTypes: file_google_genomics_v1_reads_proto_goTypes, |
| DependencyIndexes: file_google_genomics_v1_reads_proto_depIdxs, |
| EnumInfos: file_google_genomics_v1_reads_proto_enumTypes, |
| MessageInfos: file_google_genomics_v1_reads_proto_msgTypes, |
| }.Build() |
| File_google_genomics_v1_reads_proto = out.File |
| file_google_genomics_v1_reads_proto_rawDesc = nil |
| file_google_genomics_v1_reads_proto_goTypes = nil |
| file_google_genomics_v1_reads_proto_depIdxs = nil |
| } |
| |
| // Reference imports to suppress errors if they are not otherwise used. |
| var _ context.Context |
| var _ grpc.ClientConnInterface |
| |
| // This is a compile-time assertion to ensure that this generated file |
| // is compatible with the grpc package it is being compiled against. |
| const _ = grpc.SupportPackageIsVersion6 |
| |
| // StreamingReadServiceClient is the client API for StreamingReadService service. |
| // |
| // For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream. |
| type StreamingReadServiceClient interface { |
| // Returns a stream of all the reads matching the search request, ordered |
| // by reference name, position, and ID. |
| StreamReads(ctx context.Context, in *StreamReadsRequest, opts ...grpc.CallOption) (StreamingReadService_StreamReadsClient, error) |
| } |
| |
| type streamingReadServiceClient struct { |
| cc grpc.ClientConnInterface |
| } |
| |
| func NewStreamingReadServiceClient(cc grpc.ClientConnInterface) StreamingReadServiceClient { |
| return &streamingReadServiceClient{cc} |
| } |
| |
| func (c *streamingReadServiceClient) StreamReads(ctx context.Context, in *StreamReadsRequest, opts ...grpc.CallOption) (StreamingReadService_StreamReadsClient, error) { |
| stream, err := c.cc.NewStream(ctx, &_StreamingReadService_serviceDesc.Streams[0], "/google.genomics.v1.StreamingReadService/StreamReads", opts...) |
| if err != nil { |
| return nil, err |
| } |
| x := &streamingReadServiceStreamReadsClient{stream} |
| if err := x.ClientStream.SendMsg(in); err != nil { |
| return nil, err |
| } |
| if err := x.ClientStream.CloseSend(); err != nil { |
| return nil, err |
| } |
| return x, nil |
| } |
| |
| type StreamingReadService_StreamReadsClient interface { |
| Recv() (*StreamReadsResponse, error) |
| grpc.ClientStream |
| } |
| |
| type streamingReadServiceStreamReadsClient struct { |
| grpc.ClientStream |
| } |
| |
| func (x *streamingReadServiceStreamReadsClient) Recv() (*StreamReadsResponse, error) { |
| m := new(StreamReadsResponse) |
| if err := x.ClientStream.RecvMsg(m); err != nil { |
| return nil, err |
| } |
| return m, nil |
| } |
| |
| // StreamingReadServiceServer is the server API for StreamingReadService service. |
| type StreamingReadServiceServer interface { |
| // Returns a stream of all the reads matching the search request, ordered |
| // by reference name, position, and ID. |
| StreamReads(*StreamReadsRequest, StreamingReadService_StreamReadsServer) error |
| } |
| |
| // UnimplementedStreamingReadServiceServer can be embedded to have forward compatible implementations. |
| type UnimplementedStreamingReadServiceServer struct { |
| } |
| |
| func (*UnimplementedStreamingReadServiceServer) StreamReads(*StreamReadsRequest, StreamingReadService_StreamReadsServer) error { |
| return status.Errorf(codes.Unimplemented, "method StreamReads not implemented") |
| } |
| |
| func RegisterStreamingReadServiceServer(s *grpc.Server, srv StreamingReadServiceServer) { |
| s.RegisterService(&_StreamingReadService_serviceDesc, srv) |
| } |
| |
| func _StreamingReadService_StreamReads_Handler(srv interface{}, stream grpc.ServerStream) error { |
| m := new(StreamReadsRequest) |
| if err := stream.RecvMsg(m); err != nil { |
| return err |
| } |
| return srv.(StreamingReadServiceServer).StreamReads(m, &streamingReadServiceStreamReadsServer{stream}) |
| } |
| |
| type StreamingReadService_StreamReadsServer interface { |
| Send(*StreamReadsResponse) error |
| grpc.ServerStream |
| } |
| |
| type streamingReadServiceStreamReadsServer struct { |
| grpc.ServerStream |
| } |
| |
| func (x *streamingReadServiceStreamReadsServer) Send(m *StreamReadsResponse) error { |
| return x.ServerStream.SendMsg(m) |
| } |
| |
| var _StreamingReadService_serviceDesc = grpc.ServiceDesc{ |
| ServiceName: "google.genomics.v1.StreamingReadService", |
| HandlerType: (*StreamingReadServiceServer)(nil), |
| Methods: []grpc.MethodDesc{}, |
| Streams: []grpc.StreamDesc{ |
| { |
| StreamName: "StreamReads", |
| Handler: _StreamingReadService_StreamReads_Handler, |
| ServerStreams: true, |
| }, |
| }, |
| Metadata: "google/genomics/v1/reads.proto", |
| } |
| |
| // ReadServiceV1Client is the client API for ReadServiceV1 service. |
| // |
| // For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream. |
| type ReadServiceV1Client interface { |
| // Creates read group sets by asynchronously importing the provided |
| // information. |
| // |
| // For the definitions of read group sets and other genomics resources, see |
| // [Fundamentals of Google |
| // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| // |
| // The caller must have WRITE permissions to the dataset. |
| // |
| // ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import |
| // |
| // - Tags will be converted to strings - tag types are not preserved |
| // - Comments (`@CO`) in the input file header will not be preserved |
| // - Original header order of references (`@SQ`) will not be preserved |
| // - Any reverse stranded unmapped reads will be reverse complemented, and |
| // their qualities (also the "BQ" and "OQ" tags, if any) will be reversed |
| // - Unmapped reads will be stripped of positional information (reference name |
| // and position) |
| ImportReadGroupSets(ctx context.Context, in *ImportReadGroupSetsRequest, opts ...grpc.CallOption) (*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) (*empty.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) |
| } |
| |
| type readServiceV1Client struct { |
| cc grpc.ClientConnInterface |
| } |
| |
| func NewReadServiceV1Client(cc grpc.ClientConnInterface) ReadServiceV1Client { |
| return &readServiceV1Client{cc} |
| } |
| |
| func (c *readServiceV1Client) ImportReadGroupSets(ctx context.Context, in *ImportReadGroupSetsRequest, opts ...grpc.CallOption) (*longrunning.Operation, error) { |
| out := new(longrunning.Operation) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/ImportReadGroupSets", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| func (c *readServiceV1Client) ExportReadGroupSet(ctx context.Context, in *ExportReadGroupSetRequest, opts ...grpc.CallOption) (*longrunning.Operation, error) { |
| out := new(longrunning.Operation) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/ExportReadGroupSet", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| func (c *readServiceV1Client) SearchReadGroupSets(ctx context.Context, in *SearchReadGroupSetsRequest, opts ...grpc.CallOption) (*SearchReadGroupSetsResponse, error) { |
| out := new(SearchReadGroupSetsResponse) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/SearchReadGroupSets", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| func (c *readServiceV1Client) UpdateReadGroupSet(ctx context.Context, in *UpdateReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error) { |
| out := new(ReadGroupSet) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/UpdateReadGroupSet", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| func (c *readServiceV1Client) DeleteReadGroupSet(ctx context.Context, in *DeleteReadGroupSetRequest, opts ...grpc.CallOption) (*empty.Empty, error) { |
| out := new(empty.Empty) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/DeleteReadGroupSet", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| func (c *readServiceV1Client) GetReadGroupSet(ctx context.Context, in *GetReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error) { |
| out := new(ReadGroupSet) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/GetReadGroupSet", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| func (c *readServiceV1Client) ListCoverageBuckets(ctx context.Context, in *ListCoverageBucketsRequest, opts ...grpc.CallOption) (*ListCoverageBucketsResponse, error) { |
| out := new(ListCoverageBucketsResponse) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/ListCoverageBuckets", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| func (c *readServiceV1Client) SearchReads(ctx context.Context, in *SearchReadsRequest, opts ...grpc.CallOption) (*SearchReadsResponse, error) { |
| out := new(SearchReadsResponse) |
| err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/SearchReads", in, out, opts...) |
| if err != nil { |
| return nil, err |
| } |
| return out, nil |
| } |
| |
| // ReadServiceV1Server is the server API for ReadServiceV1 service. |
| type ReadServiceV1Server interface { |
| // Creates read group sets by asynchronously importing the provided |
| // information. |
| // |
| // For the definitions of read group sets and other genomics resources, see |
| // [Fundamentals of Google |
| // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| // |
| // The caller must have WRITE permissions to the dataset. |
| // |
| // ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import |
| // |
| // - Tags will be converted to strings - tag types are not preserved |
| // - Comments (`@CO`) in the input file header will not be preserved |
| // - Original header order of references (`@SQ`) will not be preserved |
| // - Any reverse stranded unmapped reads will be reverse complemented, and |
| // their qualities (also the "BQ" and "OQ" tags, if any) will be reversed |
| // - Unmapped reads will be stripped of positional information (reference name |
| // and position) |
| ImportReadGroupSets(context.Context, *ImportReadGroupSetsRequest) (*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) (*empty.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) |
| } |
| |
| // UnimplementedReadServiceV1Server can be embedded to have forward compatible implementations. |
| type UnimplementedReadServiceV1Server struct { |
| } |
| |
| func (*UnimplementedReadServiceV1Server) ImportReadGroupSets(context.Context, *ImportReadGroupSetsRequest) (*longrunning.Operation, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method ImportReadGroupSets not implemented") |
| } |
| func (*UnimplementedReadServiceV1Server) ExportReadGroupSet(context.Context, *ExportReadGroupSetRequest) (*longrunning.Operation, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method ExportReadGroupSet not implemented") |
| } |
| func (*UnimplementedReadServiceV1Server) SearchReadGroupSets(context.Context, *SearchReadGroupSetsRequest) (*SearchReadGroupSetsResponse, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method SearchReadGroupSets not implemented") |
| } |
| func (*UnimplementedReadServiceV1Server) UpdateReadGroupSet(context.Context, *UpdateReadGroupSetRequest) (*ReadGroupSet, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method UpdateReadGroupSet not implemented") |
| } |
| func (*UnimplementedReadServiceV1Server) DeleteReadGroupSet(context.Context, *DeleteReadGroupSetRequest) (*empty.Empty, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method DeleteReadGroupSet not implemented") |
| } |
| func (*UnimplementedReadServiceV1Server) GetReadGroupSet(context.Context, *GetReadGroupSetRequest) (*ReadGroupSet, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method GetReadGroupSet not implemented") |
| } |
| func (*UnimplementedReadServiceV1Server) ListCoverageBuckets(context.Context, *ListCoverageBucketsRequest) (*ListCoverageBucketsResponse, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method ListCoverageBuckets not implemented") |
| } |
| func (*UnimplementedReadServiceV1Server) SearchReads(context.Context, *SearchReadsRequest) (*SearchReadsResponse, error) { |
| return nil, status.Errorf(codes.Unimplemented, "method SearchReads not implemented") |
| } |
| |
| func RegisterReadServiceV1Server(s *grpc.Server, srv ReadServiceV1Server) { |
| s.RegisterService(&_ReadServiceV1_serviceDesc, srv) |
| } |
| |
| func _ReadServiceV1_ImportReadGroupSets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(ImportReadGroupSetsRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).ImportReadGroupSets(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/ImportReadGroupSets", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).ImportReadGroupSets(ctx, req.(*ImportReadGroupSetsRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| func _ReadServiceV1_ExportReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(ExportReadGroupSetRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).ExportReadGroupSet(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/ExportReadGroupSet", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).ExportReadGroupSet(ctx, req.(*ExportReadGroupSetRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| func _ReadServiceV1_SearchReadGroupSets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(SearchReadGroupSetsRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).SearchReadGroupSets(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/SearchReadGroupSets", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).SearchReadGroupSets(ctx, req.(*SearchReadGroupSetsRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| func _ReadServiceV1_UpdateReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(UpdateReadGroupSetRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).UpdateReadGroupSet(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/UpdateReadGroupSet", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).UpdateReadGroupSet(ctx, req.(*UpdateReadGroupSetRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| func _ReadServiceV1_DeleteReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(DeleteReadGroupSetRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).DeleteReadGroupSet(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/DeleteReadGroupSet", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).DeleteReadGroupSet(ctx, req.(*DeleteReadGroupSetRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| func _ReadServiceV1_GetReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(GetReadGroupSetRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).GetReadGroupSet(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/GetReadGroupSet", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).GetReadGroupSet(ctx, req.(*GetReadGroupSetRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| func _ReadServiceV1_ListCoverageBuckets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(ListCoverageBucketsRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).ListCoverageBuckets(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/ListCoverageBuckets", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).ListCoverageBuckets(ctx, req.(*ListCoverageBucketsRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| func _ReadServiceV1_SearchReads_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { |
| in := new(SearchReadsRequest) |
| if err := dec(in); err != nil { |
| return nil, err |
| } |
| if interceptor == nil { |
| return srv.(ReadServiceV1Server).SearchReads(ctx, in) |
| } |
| info := &grpc.UnaryServerInfo{ |
| Server: srv, |
| FullMethod: "/google.genomics.v1.ReadServiceV1/SearchReads", |
| } |
| handler := func(ctx context.Context, req interface{}) (interface{}, error) { |
| return srv.(ReadServiceV1Server).SearchReads(ctx, req.(*SearchReadsRequest)) |
| } |
| return interceptor(ctx, in, info, handler) |
| } |
| |
| var _ReadServiceV1_serviceDesc = grpc.ServiceDesc{ |
| ServiceName: "google.genomics.v1.ReadServiceV1", |
| HandlerType: (*ReadServiceV1Server)(nil), |
| Methods: []grpc.MethodDesc{ |
| { |
| MethodName: "ImportReadGroupSets", |
| Handler: _ReadServiceV1_ImportReadGroupSets_Handler, |
| }, |
| { |
| MethodName: "ExportReadGroupSet", |
| Handler: _ReadServiceV1_ExportReadGroupSet_Handler, |
| }, |
| { |
| MethodName: "SearchReadGroupSets", |
| Handler: _ReadServiceV1_SearchReadGroupSets_Handler, |
| }, |
| { |
| MethodName: "UpdateReadGroupSet", |
| Handler: _ReadServiceV1_UpdateReadGroupSet_Handler, |
| }, |
| { |
| MethodName: "DeleteReadGroupSet", |
| Handler: _ReadServiceV1_DeleteReadGroupSet_Handler, |
| }, |
| { |
| MethodName: "GetReadGroupSet", |
| Handler: _ReadServiceV1_GetReadGroupSet_Handler, |
| }, |
| { |
| MethodName: "ListCoverageBuckets", |
| Handler: _ReadServiceV1_ListCoverageBuckets_Handler, |
| }, |
| { |
| MethodName: "SearchReads", |
| Handler: _ReadServiceV1_SearchReads_Handler, |
| }, |
| }, |
| Streams: []grpc.StreamDesc{}, |
| Metadata: "google/genomics/v1/reads.proto", |
| } |