1// Copyright 2016 Google Inc. 2// 3// Licensed under the Apache License, Version 2.0 (the "License"); 4// you may not use this file except in compliance with the License. 5// You may obtain a copy of the License at 6// 7// http://www.apache.org/licenses/LICENSE-2.0 8// 9// Unless required by applicable law or agreed to in writing, software 10// distributed under the License is distributed on an "AS IS" BASIS, 11// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12// See the License for the specific language governing permissions and 13// limitations under the License. 14 15// Code generated by protoc-gen-go. DO NOT EDIT. 16// versions: 17// protoc-gen-go v1.26.0 18// protoc v3.12.2 19// source: google/genomics/v1/reads.proto 20 21package genomics 22 23import ( 24 context "context" 25 reflect "reflect" 26 sync "sync" 27 28 _ "google.golang.org/genproto/googleapis/api/annotations" 29 longrunning "google.golang.org/genproto/googleapis/longrunning" 30 grpc "google.golang.org/grpc" 31 codes "google.golang.org/grpc/codes" 32 status "google.golang.org/grpc/status" 33 protoreflect "google.golang.org/protobuf/reflect/protoreflect" 34 protoimpl "google.golang.org/protobuf/runtime/protoimpl" 35 emptypb "google.golang.org/protobuf/types/known/emptypb" 36 fieldmaskpb "google.golang.org/protobuf/types/known/fieldmaskpb" 37) 38 39const ( 40 // Verify that this generated code is sufficiently up-to-date. 41 _ = protoimpl.EnforceVersion(20 - protoimpl.MinVersion) 42 // Verify that runtime/protoimpl is sufficiently up-to-date. 43 _ = protoimpl.EnforceVersion(protoimpl.MaxVersion - 20) 44) 45 46type ImportReadGroupSetsRequest_PartitionStrategy int32 47 48const ( 49 ImportReadGroupSetsRequest_PARTITION_STRATEGY_UNSPECIFIED ImportReadGroupSetsRequest_PartitionStrategy = 0 50 // In most cases, this strategy yields one read group set per file. This is 51 // the default behavior. 52 // 53 // Allocate one read group set per file per sample. For BAM files, read 54 // groups are considered to share a sample if they have identical sample 55 // names. Furthermore, all reads for each file which do not belong to a read 56 // group, if any, will be grouped into a single read group set per-file. 57 ImportReadGroupSetsRequest_PER_FILE_PER_SAMPLE ImportReadGroupSetsRequest_PartitionStrategy = 1 58 // Includes all read groups in all imported files into a single read group 59 // set. Requires that the headers for all imported files are equivalent. All 60 // reads which do not belong to a read group, if any, will be grouped into a 61 // separate read group set. 62 ImportReadGroupSetsRequest_MERGE_ALL ImportReadGroupSetsRequest_PartitionStrategy = 2 63) 64 65// Enum value maps for ImportReadGroupSetsRequest_PartitionStrategy. 66var ( 67 ImportReadGroupSetsRequest_PartitionStrategy_name = map[int32]string{ 68 0: "PARTITION_STRATEGY_UNSPECIFIED", 69 1: "PER_FILE_PER_SAMPLE", 70 2: "MERGE_ALL", 71 } 72 ImportReadGroupSetsRequest_PartitionStrategy_value = map[string]int32{ 73 "PARTITION_STRATEGY_UNSPECIFIED": 0, 74 "PER_FILE_PER_SAMPLE": 1, 75 "MERGE_ALL": 2, 76 } 77) 78 79func (x ImportReadGroupSetsRequest_PartitionStrategy) Enum() *ImportReadGroupSetsRequest_PartitionStrategy { 80 p := new(ImportReadGroupSetsRequest_PartitionStrategy) 81 *p = x 82 return p 83} 84 85func (x ImportReadGroupSetsRequest_PartitionStrategy) String() string { 86 return protoimpl.X.EnumStringOf(x.Descriptor(), protoreflect.EnumNumber(x)) 87} 88 89func (ImportReadGroupSetsRequest_PartitionStrategy) Descriptor() protoreflect.EnumDescriptor { 90 return file_google_genomics_v1_reads_proto_enumTypes[0].Descriptor() 91} 92 93func (ImportReadGroupSetsRequest_PartitionStrategy) Type() protoreflect.EnumType { 94 return &file_google_genomics_v1_reads_proto_enumTypes[0] 95} 96 97func (x ImportReadGroupSetsRequest_PartitionStrategy) Number() protoreflect.EnumNumber { 98 return protoreflect.EnumNumber(x) 99} 100 101// Deprecated: Use ImportReadGroupSetsRequest_PartitionStrategy.Descriptor instead. 102func (ImportReadGroupSetsRequest_PartitionStrategy) EnumDescriptor() ([]byte, []int) { 103 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{2, 0} 104} 105 106// The read group set search request. 107type SearchReadGroupSetsRequest struct { 108 state protoimpl.MessageState 109 sizeCache protoimpl.SizeCache 110 unknownFields protoimpl.UnknownFields 111 112 // Restricts this query to read group sets within the given datasets. At least 113 // one ID must be provided. 114 DatasetIds []string `protobuf:"bytes,1,rep,name=dataset_ids,json=datasetIds,proto3" json:"dataset_ids,omitempty"` 115 // Only return read group sets for which a substring of the name matches this 116 // string. 117 Name string `protobuf:"bytes,3,opt,name=name,proto3" json:"name,omitempty"` 118 // The continuation token, which is used to page through large result sets. 119 // To get the next page of results, set this parameter to the value of 120 // `nextPageToken` from the previous response. 121 PageToken string `protobuf:"bytes,2,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"` 122 // The maximum number of results to return in a single page. If unspecified, 123 // defaults to 256. The maximum value is 1024. 124 PageSize int32 `protobuf:"varint,4,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"` 125} 126 127func (x *SearchReadGroupSetsRequest) Reset() { 128 *x = SearchReadGroupSetsRequest{} 129 if protoimpl.UnsafeEnabled { 130 mi := &file_google_genomics_v1_reads_proto_msgTypes[0] 131 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 132 ms.StoreMessageInfo(mi) 133 } 134} 135 136func (x *SearchReadGroupSetsRequest) String() string { 137 return protoimpl.X.MessageStringOf(x) 138} 139 140func (*SearchReadGroupSetsRequest) ProtoMessage() {} 141 142func (x *SearchReadGroupSetsRequest) ProtoReflect() protoreflect.Message { 143 mi := &file_google_genomics_v1_reads_proto_msgTypes[0] 144 if protoimpl.UnsafeEnabled && x != nil { 145 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 146 if ms.LoadMessageInfo() == nil { 147 ms.StoreMessageInfo(mi) 148 } 149 return ms 150 } 151 return mi.MessageOf(x) 152} 153 154// Deprecated: Use SearchReadGroupSetsRequest.ProtoReflect.Descriptor instead. 155func (*SearchReadGroupSetsRequest) Descriptor() ([]byte, []int) { 156 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{0} 157} 158 159func (x *SearchReadGroupSetsRequest) GetDatasetIds() []string { 160 if x != nil { 161 return x.DatasetIds 162 } 163 return nil 164} 165 166func (x *SearchReadGroupSetsRequest) GetName() string { 167 if x != nil { 168 return x.Name 169 } 170 return "" 171} 172 173func (x *SearchReadGroupSetsRequest) GetPageToken() string { 174 if x != nil { 175 return x.PageToken 176 } 177 return "" 178} 179 180func (x *SearchReadGroupSetsRequest) GetPageSize() int32 { 181 if x != nil { 182 return x.PageSize 183 } 184 return 0 185} 186 187// The read group set search response. 188type SearchReadGroupSetsResponse struct { 189 state protoimpl.MessageState 190 sizeCache protoimpl.SizeCache 191 unknownFields protoimpl.UnknownFields 192 193 // The list of matching read group sets. 194 ReadGroupSets []*ReadGroupSet `protobuf:"bytes,1,rep,name=read_group_sets,json=readGroupSets,proto3" json:"read_group_sets,omitempty"` 195 // The continuation token, which is used to page through large result sets. 196 // Provide this value in a subsequent request to return the next page of 197 // results. This field will be empty if there aren't any additional results. 198 NextPageToken string `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"` 199} 200 201func (x *SearchReadGroupSetsResponse) Reset() { 202 *x = SearchReadGroupSetsResponse{} 203 if protoimpl.UnsafeEnabled { 204 mi := &file_google_genomics_v1_reads_proto_msgTypes[1] 205 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 206 ms.StoreMessageInfo(mi) 207 } 208} 209 210func (x *SearchReadGroupSetsResponse) String() string { 211 return protoimpl.X.MessageStringOf(x) 212} 213 214func (*SearchReadGroupSetsResponse) ProtoMessage() {} 215 216func (x *SearchReadGroupSetsResponse) ProtoReflect() protoreflect.Message { 217 mi := &file_google_genomics_v1_reads_proto_msgTypes[1] 218 if protoimpl.UnsafeEnabled && x != nil { 219 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 220 if ms.LoadMessageInfo() == nil { 221 ms.StoreMessageInfo(mi) 222 } 223 return ms 224 } 225 return mi.MessageOf(x) 226} 227 228// Deprecated: Use SearchReadGroupSetsResponse.ProtoReflect.Descriptor instead. 229func (*SearchReadGroupSetsResponse) Descriptor() ([]byte, []int) { 230 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{1} 231} 232 233func (x *SearchReadGroupSetsResponse) GetReadGroupSets() []*ReadGroupSet { 234 if x != nil { 235 return x.ReadGroupSets 236 } 237 return nil 238} 239 240func (x *SearchReadGroupSetsResponse) GetNextPageToken() string { 241 if x != nil { 242 return x.NextPageToken 243 } 244 return "" 245} 246 247// The read group set import request. 248type ImportReadGroupSetsRequest struct { 249 state protoimpl.MessageState 250 sizeCache protoimpl.SizeCache 251 unknownFields protoimpl.UnknownFields 252 253 // Required. The ID of the dataset these read group sets will belong to. The 254 // caller must have WRITE permissions to this dataset. 255 DatasetId string `protobuf:"bytes,1,opt,name=dataset_id,json=datasetId,proto3" json:"dataset_id,omitempty"` 256 // The reference set to which the imported read group sets are aligned to, if 257 // any. The reference names of this reference set must be a superset of those 258 // found in the imported file headers. If no reference set id is provided, a 259 // best effort is made to associate with a matching reference set. 260 ReferenceSetId string `protobuf:"bytes,4,opt,name=reference_set_id,json=referenceSetId,proto3" json:"reference_set_id,omitempty"` 261 // A list of URIs pointing at [BAM 262 // files](https://samtools.github.io/hts-specs/SAMv1.pdf) 263 // in Google Cloud Storage. 264 // Those URIs can include wildcards (*), but do not add or remove 265 // matching files before import has completed. 266 // 267 // Note that Google Cloud Storage object listing is only eventually 268 // consistent: files added may be not be immediately visible to 269 // everyone. Thus, if using a wildcard it is preferable not to start 270 // the import immediately after the files are created. 271 SourceUris []string `protobuf:"bytes,2,rep,name=source_uris,json=sourceUris,proto3" json:"source_uris,omitempty"` 272 // The partition strategy describes how read groups are partitioned into read 273 // group sets. 274 PartitionStrategy ImportReadGroupSetsRequest_PartitionStrategy `protobuf:"varint,5,opt,name=partition_strategy,json=partitionStrategy,proto3,enum=google.genomics.v1.ImportReadGroupSetsRequest_PartitionStrategy" json:"partition_strategy,omitempty"` 275} 276 277func (x *ImportReadGroupSetsRequest) Reset() { 278 *x = ImportReadGroupSetsRequest{} 279 if protoimpl.UnsafeEnabled { 280 mi := &file_google_genomics_v1_reads_proto_msgTypes[2] 281 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 282 ms.StoreMessageInfo(mi) 283 } 284} 285 286func (x *ImportReadGroupSetsRequest) String() string { 287 return protoimpl.X.MessageStringOf(x) 288} 289 290func (*ImportReadGroupSetsRequest) ProtoMessage() {} 291 292func (x *ImportReadGroupSetsRequest) ProtoReflect() protoreflect.Message { 293 mi := &file_google_genomics_v1_reads_proto_msgTypes[2] 294 if protoimpl.UnsafeEnabled && x != nil { 295 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 296 if ms.LoadMessageInfo() == nil { 297 ms.StoreMessageInfo(mi) 298 } 299 return ms 300 } 301 return mi.MessageOf(x) 302} 303 304// Deprecated: Use ImportReadGroupSetsRequest.ProtoReflect.Descriptor instead. 305func (*ImportReadGroupSetsRequest) Descriptor() ([]byte, []int) { 306 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{2} 307} 308 309func (x *ImportReadGroupSetsRequest) GetDatasetId() string { 310 if x != nil { 311 return x.DatasetId 312 } 313 return "" 314} 315 316func (x *ImportReadGroupSetsRequest) GetReferenceSetId() string { 317 if x != nil { 318 return x.ReferenceSetId 319 } 320 return "" 321} 322 323func (x *ImportReadGroupSetsRequest) GetSourceUris() []string { 324 if x != nil { 325 return x.SourceUris 326 } 327 return nil 328} 329 330func (x *ImportReadGroupSetsRequest) GetPartitionStrategy() ImportReadGroupSetsRequest_PartitionStrategy { 331 if x != nil { 332 return x.PartitionStrategy 333 } 334 return ImportReadGroupSetsRequest_PARTITION_STRATEGY_UNSPECIFIED 335} 336 337// The read group set import response. 338type ImportReadGroupSetsResponse struct { 339 state protoimpl.MessageState 340 sizeCache protoimpl.SizeCache 341 unknownFields protoimpl.UnknownFields 342 343 // IDs of the read group sets that were created. 344 ReadGroupSetIds []string `protobuf:"bytes,1,rep,name=read_group_set_ids,json=readGroupSetIds,proto3" json:"read_group_set_ids,omitempty"` 345} 346 347func (x *ImportReadGroupSetsResponse) Reset() { 348 *x = ImportReadGroupSetsResponse{} 349 if protoimpl.UnsafeEnabled { 350 mi := &file_google_genomics_v1_reads_proto_msgTypes[3] 351 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 352 ms.StoreMessageInfo(mi) 353 } 354} 355 356func (x *ImportReadGroupSetsResponse) String() string { 357 return protoimpl.X.MessageStringOf(x) 358} 359 360func (*ImportReadGroupSetsResponse) ProtoMessage() {} 361 362func (x *ImportReadGroupSetsResponse) ProtoReflect() protoreflect.Message { 363 mi := &file_google_genomics_v1_reads_proto_msgTypes[3] 364 if protoimpl.UnsafeEnabled && x != nil { 365 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 366 if ms.LoadMessageInfo() == nil { 367 ms.StoreMessageInfo(mi) 368 } 369 return ms 370 } 371 return mi.MessageOf(x) 372} 373 374// Deprecated: Use ImportReadGroupSetsResponse.ProtoReflect.Descriptor instead. 375func (*ImportReadGroupSetsResponse) Descriptor() ([]byte, []int) { 376 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{3} 377} 378 379func (x *ImportReadGroupSetsResponse) GetReadGroupSetIds() []string { 380 if x != nil { 381 return x.ReadGroupSetIds 382 } 383 return nil 384} 385 386// The read group set export request. 387type ExportReadGroupSetRequest struct { 388 state protoimpl.MessageState 389 sizeCache protoimpl.SizeCache 390 unknownFields protoimpl.UnknownFields 391 392 // Required. The Google Cloud project ID that owns this 393 // export. The caller must have WRITE access to this project. 394 ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"` 395 // Required. A Google Cloud Storage URI for the exported BAM file. 396 // The currently authenticated user must have write access to the new file. 397 // An error will be returned if the URI already contains data. 398 ExportUri string `protobuf:"bytes,2,opt,name=export_uri,json=exportUri,proto3" json:"export_uri,omitempty"` 399 // Required. The ID of the read group set to export. The caller must have 400 // READ access to this read group set. 401 ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` 402 // The reference names to export. If this is not specified, all reference 403 // sequences, including unmapped reads, are exported. 404 // Use `*` to export only unmapped reads. 405 ReferenceNames []string `protobuf:"bytes,4,rep,name=reference_names,json=referenceNames,proto3" json:"reference_names,omitempty"` 406} 407 408func (x *ExportReadGroupSetRequest) Reset() { 409 *x = ExportReadGroupSetRequest{} 410 if protoimpl.UnsafeEnabled { 411 mi := &file_google_genomics_v1_reads_proto_msgTypes[4] 412 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 413 ms.StoreMessageInfo(mi) 414 } 415} 416 417func (x *ExportReadGroupSetRequest) String() string { 418 return protoimpl.X.MessageStringOf(x) 419} 420 421func (*ExportReadGroupSetRequest) ProtoMessage() {} 422 423func (x *ExportReadGroupSetRequest) ProtoReflect() protoreflect.Message { 424 mi := &file_google_genomics_v1_reads_proto_msgTypes[4] 425 if protoimpl.UnsafeEnabled && x != nil { 426 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 427 if ms.LoadMessageInfo() == nil { 428 ms.StoreMessageInfo(mi) 429 } 430 return ms 431 } 432 return mi.MessageOf(x) 433} 434 435// Deprecated: Use ExportReadGroupSetRequest.ProtoReflect.Descriptor instead. 436func (*ExportReadGroupSetRequest) Descriptor() ([]byte, []int) { 437 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{4} 438} 439 440func (x *ExportReadGroupSetRequest) GetProjectId() string { 441 if x != nil { 442 return x.ProjectId 443 } 444 return "" 445} 446 447func (x *ExportReadGroupSetRequest) GetExportUri() string { 448 if x != nil { 449 return x.ExportUri 450 } 451 return "" 452} 453 454func (x *ExportReadGroupSetRequest) GetReadGroupSetId() string { 455 if x != nil { 456 return x.ReadGroupSetId 457 } 458 return "" 459} 460 461func (x *ExportReadGroupSetRequest) GetReferenceNames() []string { 462 if x != nil { 463 return x.ReferenceNames 464 } 465 return nil 466} 467 468type UpdateReadGroupSetRequest struct { 469 state protoimpl.MessageState 470 sizeCache protoimpl.SizeCache 471 unknownFields protoimpl.UnknownFields 472 473 // The ID of the read group set to be updated. The caller must have WRITE 474 // permissions to the dataset associated with this read group set. 475 ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` 476 // The new read group set data. See `updateMask` for details on mutability of 477 // fields. 478 ReadGroupSet *ReadGroupSet `protobuf:"bytes,2,opt,name=read_group_set,json=readGroupSet,proto3" json:"read_group_set,omitempty"` 479 // An optional mask specifying which fields to update. Supported fields: 480 // 481 // * [name][google.genomics.v1.ReadGroupSet.name]. 482 // * [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id]. 483 // 484 // Leaving `updateMask` unset is equivalent to specifying all mutable 485 // fields. 486 UpdateMask *fieldmaskpb.FieldMask `protobuf:"bytes,3,opt,name=update_mask,json=updateMask,proto3" json:"update_mask,omitempty"` 487} 488 489func (x *UpdateReadGroupSetRequest) Reset() { 490 *x = UpdateReadGroupSetRequest{} 491 if protoimpl.UnsafeEnabled { 492 mi := &file_google_genomics_v1_reads_proto_msgTypes[5] 493 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 494 ms.StoreMessageInfo(mi) 495 } 496} 497 498func (x *UpdateReadGroupSetRequest) String() string { 499 return protoimpl.X.MessageStringOf(x) 500} 501 502func (*UpdateReadGroupSetRequest) ProtoMessage() {} 503 504func (x *UpdateReadGroupSetRequest) ProtoReflect() protoreflect.Message { 505 mi := &file_google_genomics_v1_reads_proto_msgTypes[5] 506 if protoimpl.UnsafeEnabled && x != nil { 507 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 508 if ms.LoadMessageInfo() == nil { 509 ms.StoreMessageInfo(mi) 510 } 511 return ms 512 } 513 return mi.MessageOf(x) 514} 515 516// Deprecated: Use UpdateReadGroupSetRequest.ProtoReflect.Descriptor instead. 517func (*UpdateReadGroupSetRequest) Descriptor() ([]byte, []int) { 518 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{5} 519} 520 521func (x *UpdateReadGroupSetRequest) GetReadGroupSetId() string { 522 if x != nil { 523 return x.ReadGroupSetId 524 } 525 return "" 526} 527 528func (x *UpdateReadGroupSetRequest) GetReadGroupSet() *ReadGroupSet { 529 if x != nil { 530 return x.ReadGroupSet 531 } 532 return nil 533} 534 535func (x *UpdateReadGroupSetRequest) GetUpdateMask() *fieldmaskpb.FieldMask { 536 if x != nil { 537 return x.UpdateMask 538 } 539 return nil 540} 541 542type DeleteReadGroupSetRequest struct { 543 state protoimpl.MessageState 544 sizeCache protoimpl.SizeCache 545 unknownFields protoimpl.UnknownFields 546 547 // The ID of the read group set to be deleted. The caller must have WRITE 548 // permissions to the dataset associated with this read group set. 549 ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` 550} 551 552func (x *DeleteReadGroupSetRequest) Reset() { 553 *x = DeleteReadGroupSetRequest{} 554 if protoimpl.UnsafeEnabled { 555 mi := &file_google_genomics_v1_reads_proto_msgTypes[6] 556 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 557 ms.StoreMessageInfo(mi) 558 } 559} 560 561func (x *DeleteReadGroupSetRequest) String() string { 562 return protoimpl.X.MessageStringOf(x) 563} 564 565func (*DeleteReadGroupSetRequest) ProtoMessage() {} 566 567func (x *DeleteReadGroupSetRequest) ProtoReflect() protoreflect.Message { 568 mi := &file_google_genomics_v1_reads_proto_msgTypes[6] 569 if protoimpl.UnsafeEnabled && x != nil { 570 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 571 if ms.LoadMessageInfo() == nil { 572 ms.StoreMessageInfo(mi) 573 } 574 return ms 575 } 576 return mi.MessageOf(x) 577} 578 579// Deprecated: Use DeleteReadGroupSetRequest.ProtoReflect.Descriptor instead. 580func (*DeleteReadGroupSetRequest) Descriptor() ([]byte, []int) { 581 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{6} 582} 583 584func (x *DeleteReadGroupSetRequest) GetReadGroupSetId() string { 585 if x != nil { 586 return x.ReadGroupSetId 587 } 588 return "" 589} 590 591type GetReadGroupSetRequest struct { 592 state protoimpl.MessageState 593 sizeCache protoimpl.SizeCache 594 unknownFields protoimpl.UnknownFields 595 596 // The ID of the read group set. 597 ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` 598} 599 600func (x *GetReadGroupSetRequest) Reset() { 601 *x = GetReadGroupSetRequest{} 602 if protoimpl.UnsafeEnabled { 603 mi := &file_google_genomics_v1_reads_proto_msgTypes[7] 604 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 605 ms.StoreMessageInfo(mi) 606 } 607} 608 609func (x *GetReadGroupSetRequest) String() string { 610 return protoimpl.X.MessageStringOf(x) 611} 612 613func (*GetReadGroupSetRequest) ProtoMessage() {} 614 615func (x *GetReadGroupSetRequest) ProtoReflect() protoreflect.Message { 616 mi := &file_google_genomics_v1_reads_proto_msgTypes[7] 617 if protoimpl.UnsafeEnabled && x != nil { 618 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 619 if ms.LoadMessageInfo() == nil { 620 ms.StoreMessageInfo(mi) 621 } 622 return ms 623 } 624 return mi.MessageOf(x) 625} 626 627// Deprecated: Use GetReadGroupSetRequest.ProtoReflect.Descriptor instead. 628func (*GetReadGroupSetRequest) Descriptor() ([]byte, []int) { 629 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{7} 630} 631 632func (x *GetReadGroupSetRequest) GetReadGroupSetId() string { 633 if x != nil { 634 return x.ReadGroupSetId 635 } 636 return "" 637} 638 639type ListCoverageBucketsRequest struct { 640 state protoimpl.MessageState 641 sizeCache protoimpl.SizeCache 642 unknownFields protoimpl.UnknownFields 643 644 // Required. The ID of the read group set over which coverage is requested. 645 ReadGroupSetId string `protobuf:"bytes,1,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` 646 // The name of the reference to query, within the reference set associated 647 // with this query. Optional. 648 ReferenceName string `protobuf:"bytes,3,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"` 649 // The start position of the range on the reference, 0-based inclusive. If 650 // specified, `referenceName` must also be specified. Defaults to 0. 651 Start int64 `protobuf:"varint,4,opt,name=start,proto3" json:"start,omitempty"` 652 // The end position of the range on the reference, 0-based exclusive. If 653 // specified, `referenceName` must also be specified. If unset or 0, defaults 654 // to the length of the reference. 655 End int64 `protobuf:"varint,5,opt,name=end,proto3" json:"end,omitempty"` 656 // The desired width of each reported coverage bucket in base pairs. This 657 // will be rounded down to the nearest precomputed bucket width; the value 658 // of which is returned as `bucketWidth` in the response. Defaults 659 // to infinity (each bucket spans an entire reference sequence) or the length 660 // of the target range, if specified. The smallest precomputed 661 // `bucketWidth` is currently 2048 base pairs; this is subject to 662 // change. 663 TargetBucketWidth int64 `protobuf:"varint,6,opt,name=target_bucket_width,json=targetBucketWidth,proto3" json:"target_bucket_width,omitempty"` 664 // The continuation token, which is used to page through large result sets. 665 // To get the next page of results, set this parameter to the value of 666 // `nextPageToken` from the previous response. 667 PageToken string `protobuf:"bytes,7,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"` 668 // The maximum number of results to return in a single page. If unspecified, 669 // defaults to 1024. The maximum value is 2048. 670 PageSize int32 `protobuf:"varint,8,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"` 671} 672 673func (x *ListCoverageBucketsRequest) Reset() { 674 *x = ListCoverageBucketsRequest{} 675 if protoimpl.UnsafeEnabled { 676 mi := &file_google_genomics_v1_reads_proto_msgTypes[8] 677 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 678 ms.StoreMessageInfo(mi) 679 } 680} 681 682func (x *ListCoverageBucketsRequest) String() string { 683 return protoimpl.X.MessageStringOf(x) 684} 685 686func (*ListCoverageBucketsRequest) ProtoMessage() {} 687 688func (x *ListCoverageBucketsRequest) ProtoReflect() protoreflect.Message { 689 mi := &file_google_genomics_v1_reads_proto_msgTypes[8] 690 if protoimpl.UnsafeEnabled && x != nil { 691 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 692 if ms.LoadMessageInfo() == nil { 693 ms.StoreMessageInfo(mi) 694 } 695 return ms 696 } 697 return mi.MessageOf(x) 698} 699 700// Deprecated: Use ListCoverageBucketsRequest.ProtoReflect.Descriptor instead. 701func (*ListCoverageBucketsRequest) Descriptor() ([]byte, []int) { 702 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{8} 703} 704 705func (x *ListCoverageBucketsRequest) GetReadGroupSetId() string { 706 if x != nil { 707 return x.ReadGroupSetId 708 } 709 return "" 710} 711 712func (x *ListCoverageBucketsRequest) GetReferenceName() string { 713 if x != nil { 714 return x.ReferenceName 715 } 716 return "" 717} 718 719func (x *ListCoverageBucketsRequest) GetStart() int64 { 720 if x != nil { 721 return x.Start 722 } 723 return 0 724} 725 726func (x *ListCoverageBucketsRequest) GetEnd() int64 { 727 if x != nil { 728 return x.End 729 } 730 return 0 731} 732 733func (x *ListCoverageBucketsRequest) GetTargetBucketWidth() int64 { 734 if x != nil { 735 return x.TargetBucketWidth 736 } 737 return 0 738} 739 740func (x *ListCoverageBucketsRequest) GetPageToken() string { 741 if x != nil { 742 return x.PageToken 743 } 744 return "" 745} 746 747func (x *ListCoverageBucketsRequest) GetPageSize() int32 { 748 if x != nil { 749 return x.PageSize 750 } 751 return 0 752} 753 754// A bucket over which read coverage has been precomputed. A bucket corresponds 755// to a specific range of the reference sequence. 756type CoverageBucket struct { 757 state protoimpl.MessageState 758 sizeCache protoimpl.SizeCache 759 unknownFields protoimpl.UnknownFields 760 761 // The genomic coordinate range spanned by this bucket. 762 Range *Range `protobuf:"bytes,1,opt,name=range,proto3" json:"range,omitempty"` 763 // The average number of reads which are aligned to each individual 764 // reference base in this bucket. 765 MeanCoverage float32 `protobuf:"fixed32,2,opt,name=mean_coverage,json=meanCoverage,proto3" json:"mean_coverage,omitempty"` 766} 767 768func (x *CoverageBucket) Reset() { 769 *x = CoverageBucket{} 770 if protoimpl.UnsafeEnabled { 771 mi := &file_google_genomics_v1_reads_proto_msgTypes[9] 772 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 773 ms.StoreMessageInfo(mi) 774 } 775} 776 777func (x *CoverageBucket) String() string { 778 return protoimpl.X.MessageStringOf(x) 779} 780 781func (*CoverageBucket) ProtoMessage() {} 782 783func (x *CoverageBucket) ProtoReflect() protoreflect.Message { 784 mi := &file_google_genomics_v1_reads_proto_msgTypes[9] 785 if protoimpl.UnsafeEnabled && x != nil { 786 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 787 if ms.LoadMessageInfo() == nil { 788 ms.StoreMessageInfo(mi) 789 } 790 return ms 791 } 792 return mi.MessageOf(x) 793} 794 795// Deprecated: Use CoverageBucket.ProtoReflect.Descriptor instead. 796func (*CoverageBucket) Descriptor() ([]byte, []int) { 797 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{9} 798} 799 800func (x *CoverageBucket) GetRange() *Range { 801 if x != nil { 802 return x.Range 803 } 804 return nil 805} 806 807func (x *CoverageBucket) GetMeanCoverage() float32 { 808 if x != nil { 809 return x.MeanCoverage 810 } 811 return 0 812} 813 814type ListCoverageBucketsResponse struct { 815 state protoimpl.MessageState 816 sizeCache protoimpl.SizeCache 817 unknownFields protoimpl.UnknownFields 818 819 // The length of each coverage bucket in base pairs. Note that buckets at the 820 // end of a reference sequence may be shorter. This value is omitted if the 821 // bucket width is infinity (the default behaviour, with no range or 822 // `targetBucketWidth`). 823 BucketWidth int64 `protobuf:"varint,1,opt,name=bucket_width,json=bucketWidth,proto3" json:"bucket_width,omitempty"` 824 // The coverage buckets. The list of buckets is sparse; a bucket with 0 825 // overlapping reads is not returned. A bucket never crosses more than one 826 // reference sequence. Each bucket has width `bucketWidth`, unless 827 // its end is the end of the reference sequence. 828 CoverageBuckets []*CoverageBucket `protobuf:"bytes,2,rep,name=coverage_buckets,json=coverageBuckets,proto3" json:"coverage_buckets,omitempty"` 829 // The continuation token, which is used to page through large result sets. 830 // Provide this value in a subsequent request to return the next page of 831 // results. This field will be empty if there aren't any additional results. 832 NextPageToken string `protobuf:"bytes,3,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"` 833} 834 835func (x *ListCoverageBucketsResponse) Reset() { 836 *x = ListCoverageBucketsResponse{} 837 if protoimpl.UnsafeEnabled { 838 mi := &file_google_genomics_v1_reads_proto_msgTypes[10] 839 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 840 ms.StoreMessageInfo(mi) 841 } 842} 843 844func (x *ListCoverageBucketsResponse) String() string { 845 return protoimpl.X.MessageStringOf(x) 846} 847 848func (*ListCoverageBucketsResponse) ProtoMessage() {} 849 850func (x *ListCoverageBucketsResponse) ProtoReflect() protoreflect.Message { 851 mi := &file_google_genomics_v1_reads_proto_msgTypes[10] 852 if protoimpl.UnsafeEnabled && x != nil { 853 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 854 if ms.LoadMessageInfo() == nil { 855 ms.StoreMessageInfo(mi) 856 } 857 return ms 858 } 859 return mi.MessageOf(x) 860} 861 862// Deprecated: Use ListCoverageBucketsResponse.ProtoReflect.Descriptor instead. 863func (*ListCoverageBucketsResponse) Descriptor() ([]byte, []int) { 864 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{10} 865} 866 867func (x *ListCoverageBucketsResponse) GetBucketWidth() int64 { 868 if x != nil { 869 return x.BucketWidth 870 } 871 return 0 872} 873 874func (x *ListCoverageBucketsResponse) GetCoverageBuckets() []*CoverageBucket { 875 if x != nil { 876 return x.CoverageBuckets 877 } 878 return nil 879} 880 881func (x *ListCoverageBucketsResponse) GetNextPageToken() string { 882 if x != nil { 883 return x.NextPageToken 884 } 885 return "" 886} 887 888// The read search request. 889type SearchReadsRequest struct { 890 state protoimpl.MessageState 891 sizeCache protoimpl.SizeCache 892 unknownFields protoimpl.UnknownFields 893 894 // The IDs of the read groups sets within which to search for reads. All 895 // specified read group sets must be aligned against a common set of reference 896 // sequences; this defines the genomic coordinates for the query. Must specify 897 // one of `readGroupSetIds` or `readGroupIds`. 898 ReadGroupSetIds []string `protobuf:"bytes,1,rep,name=read_group_set_ids,json=readGroupSetIds,proto3" json:"read_group_set_ids,omitempty"` 899 // The IDs of the read groups within which to search for reads. All specified 900 // read groups must belong to the same read group sets. Must specify one of 901 // `readGroupSetIds` or `readGroupIds`. 902 ReadGroupIds []string `protobuf:"bytes,5,rep,name=read_group_ids,json=readGroupIds,proto3" json:"read_group_ids,omitempty"` 903 // The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to 904 // `*`, only unmapped reads are returned. If unspecified, all reads (mapped 905 // and unmapped) are returned. 906 ReferenceName string `protobuf:"bytes,7,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"` 907 // The start position of the range on the reference, 0-based inclusive. If 908 // specified, `referenceName` must also be specified. 909 Start int64 `protobuf:"varint,8,opt,name=start,proto3" json:"start,omitempty"` 910 // The end position of the range on the reference, 0-based exclusive. If 911 // specified, `referenceName` must also be specified. 912 End int64 `protobuf:"varint,9,opt,name=end,proto3" json:"end,omitempty"` 913 // The continuation token, which is used to page through large result sets. 914 // To get the next page of results, set this parameter to the value of 915 // `nextPageToken` from the previous response. 916 PageToken string `protobuf:"bytes,3,opt,name=page_token,json=pageToken,proto3" json:"page_token,omitempty"` 917 // The maximum number of results to return in a single page. If unspecified, 918 // defaults to 256. The maximum value is 2048. 919 PageSize int32 `protobuf:"varint,4,opt,name=page_size,json=pageSize,proto3" json:"page_size,omitempty"` 920} 921 922func (x *SearchReadsRequest) Reset() { 923 *x = SearchReadsRequest{} 924 if protoimpl.UnsafeEnabled { 925 mi := &file_google_genomics_v1_reads_proto_msgTypes[11] 926 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 927 ms.StoreMessageInfo(mi) 928 } 929} 930 931func (x *SearchReadsRequest) String() string { 932 return protoimpl.X.MessageStringOf(x) 933} 934 935func (*SearchReadsRequest) ProtoMessage() {} 936 937func (x *SearchReadsRequest) ProtoReflect() protoreflect.Message { 938 mi := &file_google_genomics_v1_reads_proto_msgTypes[11] 939 if protoimpl.UnsafeEnabled && x != nil { 940 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 941 if ms.LoadMessageInfo() == nil { 942 ms.StoreMessageInfo(mi) 943 } 944 return ms 945 } 946 return mi.MessageOf(x) 947} 948 949// Deprecated: Use SearchReadsRequest.ProtoReflect.Descriptor instead. 950func (*SearchReadsRequest) Descriptor() ([]byte, []int) { 951 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{11} 952} 953 954func (x *SearchReadsRequest) GetReadGroupSetIds() []string { 955 if x != nil { 956 return x.ReadGroupSetIds 957 } 958 return nil 959} 960 961func (x *SearchReadsRequest) GetReadGroupIds() []string { 962 if x != nil { 963 return x.ReadGroupIds 964 } 965 return nil 966} 967 968func (x *SearchReadsRequest) GetReferenceName() string { 969 if x != nil { 970 return x.ReferenceName 971 } 972 return "" 973} 974 975func (x *SearchReadsRequest) GetStart() int64 { 976 if x != nil { 977 return x.Start 978 } 979 return 0 980} 981 982func (x *SearchReadsRequest) GetEnd() int64 { 983 if x != nil { 984 return x.End 985 } 986 return 0 987} 988 989func (x *SearchReadsRequest) GetPageToken() string { 990 if x != nil { 991 return x.PageToken 992 } 993 return "" 994} 995 996func (x *SearchReadsRequest) GetPageSize() int32 { 997 if x != nil { 998 return x.PageSize 999 } 1000 return 0 1001} 1002 1003// The read search response. 1004type SearchReadsResponse struct { 1005 state protoimpl.MessageState 1006 sizeCache protoimpl.SizeCache 1007 unknownFields protoimpl.UnknownFields 1008 1009 // The list of matching alignments sorted by mapped genomic coordinate, 1010 // if any, ascending in position within the same reference. Unmapped reads, 1011 // which have no position, are returned contiguously and are sorted in 1012 // ascending lexicographic order by fragment name. 1013 Alignments []*Read `protobuf:"bytes,1,rep,name=alignments,proto3" json:"alignments,omitempty"` 1014 // The continuation token, which is used to page through large result sets. 1015 // Provide this value in a subsequent request to return the next page of 1016 // results. This field will be empty if there aren't any additional results. 1017 NextPageToken string `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken,proto3" json:"next_page_token,omitempty"` 1018} 1019 1020func (x *SearchReadsResponse) Reset() { 1021 *x = SearchReadsResponse{} 1022 if protoimpl.UnsafeEnabled { 1023 mi := &file_google_genomics_v1_reads_proto_msgTypes[12] 1024 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 1025 ms.StoreMessageInfo(mi) 1026 } 1027} 1028 1029func (x *SearchReadsResponse) String() string { 1030 return protoimpl.X.MessageStringOf(x) 1031} 1032 1033func (*SearchReadsResponse) ProtoMessage() {} 1034 1035func (x *SearchReadsResponse) ProtoReflect() protoreflect.Message { 1036 mi := &file_google_genomics_v1_reads_proto_msgTypes[12] 1037 if protoimpl.UnsafeEnabled && x != nil { 1038 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 1039 if ms.LoadMessageInfo() == nil { 1040 ms.StoreMessageInfo(mi) 1041 } 1042 return ms 1043 } 1044 return mi.MessageOf(x) 1045} 1046 1047// Deprecated: Use SearchReadsResponse.ProtoReflect.Descriptor instead. 1048func (*SearchReadsResponse) Descriptor() ([]byte, []int) { 1049 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{12} 1050} 1051 1052func (x *SearchReadsResponse) GetAlignments() []*Read { 1053 if x != nil { 1054 return x.Alignments 1055 } 1056 return nil 1057} 1058 1059func (x *SearchReadsResponse) GetNextPageToken() string { 1060 if x != nil { 1061 return x.NextPageToken 1062 } 1063 return "" 1064} 1065 1066// The stream reads request. 1067type StreamReadsRequest struct { 1068 state protoimpl.MessageState 1069 sizeCache protoimpl.SizeCache 1070 unknownFields protoimpl.UnknownFields 1071 1072 // The Google Cloud project ID which will be billed 1073 // for this access. The caller must have WRITE access to this project. 1074 // Required. 1075 ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId,proto3" json:"project_id,omitempty"` 1076 // The ID of the read group set from which to stream reads. 1077 ReadGroupSetId string `protobuf:"bytes,2,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"` 1078 // The reference sequence name, for example `chr1`, 1079 // `1`, or `chrX`. If set to *, only unmapped reads are 1080 // returned. 1081 ReferenceName string `protobuf:"bytes,3,opt,name=reference_name,json=referenceName,proto3" json:"reference_name,omitempty"` 1082 // The start position of the range on the reference, 0-based inclusive. If 1083 // specified, `referenceName` must also be specified. 1084 Start int64 `protobuf:"varint,4,opt,name=start,proto3" json:"start,omitempty"` 1085 // The end position of the range on the reference, 0-based exclusive. If 1086 // specified, `referenceName` must also be specified. 1087 End int64 `protobuf:"varint,5,opt,name=end,proto3" json:"end,omitempty"` 1088 // Restricts results to a shard containing approximately `1/totalShards` 1089 // of the normal response payload for this query. Results from a sharded 1090 // request are disjoint from those returned by all queries which differ only 1091 // in their shard parameter. A shard may yield 0 results; this is especially 1092 // likely for large values of `totalShards`. 1093 // 1094 // Valid values are `[0, totalShards)`. 1095 Shard int32 `protobuf:"varint,6,opt,name=shard,proto3" json:"shard,omitempty"` 1096 // Specifying `totalShards` causes a disjoint subset of the normal response 1097 // payload to be returned for each query with a unique `shard` parameter 1098 // specified. A best effort is made to yield equally sized shards. Sharding 1099 // can be used to distribute processing amongst workers, where each worker is 1100 // assigned a unique `shard` number and all workers specify the same 1101 // `totalShards` number. The union of reads returned for all sharded queries 1102 // `[0, totalShards)` is equal to those returned by a single unsharded query. 1103 // 1104 // Queries for different values of `totalShards` with common divisors will 1105 // share shard boundaries. For example, streaming `shard` 2 of 5 1106 // `totalShards` yields the same results as streaming `shard`s 4 and 5 of 10 1107 // `totalShards`. This property can be leveraged for adaptive retries. 1108 TotalShards int32 `protobuf:"varint,7,opt,name=total_shards,json=totalShards,proto3" json:"total_shards,omitempty"` 1109} 1110 1111func (x *StreamReadsRequest) Reset() { 1112 *x = StreamReadsRequest{} 1113 if protoimpl.UnsafeEnabled { 1114 mi := &file_google_genomics_v1_reads_proto_msgTypes[13] 1115 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 1116 ms.StoreMessageInfo(mi) 1117 } 1118} 1119 1120func (x *StreamReadsRequest) String() string { 1121 return protoimpl.X.MessageStringOf(x) 1122} 1123 1124func (*StreamReadsRequest) ProtoMessage() {} 1125 1126func (x *StreamReadsRequest) ProtoReflect() protoreflect.Message { 1127 mi := &file_google_genomics_v1_reads_proto_msgTypes[13] 1128 if protoimpl.UnsafeEnabled && x != nil { 1129 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 1130 if ms.LoadMessageInfo() == nil { 1131 ms.StoreMessageInfo(mi) 1132 } 1133 return ms 1134 } 1135 return mi.MessageOf(x) 1136} 1137 1138// Deprecated: Use StreamReadsRequest.ProtoReflect.Descriptor instead. 1139func (*StreamReadsRequest) Descriptor() ([]byte, []int) { 1140 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{13} 1141} 1142 1143func (x *StreamReadsRequest) GetProjectId() string { 1144 if x != nil { 1145 return x.ProjectId 1146 } 1147 return "" 1148} 1149 1150func (x *StreamReadsRequest) GetReadGroupSetId() string { 1151 if x != nil { 1152 return x.ReadGroupSetId 1153 } 1154 return "" 1155} 1156 1157func (x *StreamReadsRequest) GetReferenceName() string { 1158 if x != nil { 1159 return x.ReferenceName 1160 } 1161 return "" 1162} 1163 1164func (x *StreamReadsRequest) GetStart() int64 { 1165 if x != nil { 1166 return x.Start 1167 } 1168 return 0 1169} 1170 1171func (x *StreamReadsRequest) GetEnd() int64 { 1172 if x != nil { 1173 return x.End 1174 } 1175 return 0 1176} 1177 1178func (x *StreamReadsRequest) GetShard() int32 { 1179 if x != nil { 1180 return x.Shard 1181 } 1182 return 0 1183} 1184 1185func (x *StreamReadsRequest) GetTotalShards() int32 { 1186 if x != nil { 1187 return x.TotalShards 1188 } 1189 return 0 1190} 1191 1192type StreamReadsResponse struct { 1193 state protoimpl.MessageState 1194 sizeCache protoimpl.SizeCache 1195 unknownFields protoimpl.UnknownFields 1196 1197 Alignments []*Read `protobuf:"bytes,1,rep,name=alignments,proto3" json:"alignments,omitempty"` 1198} 1199 1200func (x *StreamReadsResponse) Reset() { 1201 *x = StreamReadsResponse{} 1202 if protoimpl.UnsafeEnabled { 1203 mi := &file_google_genomics_v1_reads_proto_msgTypes[14] 1204 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 1205 ms.StoreMessageInfo(mi) 1206 } 1207} 1208 1209func (x *StreamReadsResponse) String() string { 1210 return protoimpl.X.MessageStringOf(x) 1211} 1212 1213func (*StreamReadsResponse) ProtoMessage() {} 1214 1215func (x *StreamReadsResponse) ProtoReflect() protoreflect.Message { 1216 mi := &file_google_genomics_v1_reads_proto_msgTypes[14] 1217 if protoimpl.UnsafeEnabled && x != nil { 1218 ms := protoimpl.X.MessageStateOf(protoimpl.Pointer(x)) 1219 if ms.LoadMessageInfo() == nil { 1220 ms.StoreMessageInfo(mi) 1221 } 1222 return ms 1223 } 1224 return mi.MessageOf(x) 1225} 1226 1227// Deprecated: Use StreamReadsResponse.ProtoReflect.Descriptor instead. 1228func (*StreamReadsResponse) Descriptor() ([]byte, []int) { 1229 return file_google_genomics_v1_reads_proto_rawDescGZIP(), []int{14} 1230} 1231 1232func (x *StreamReadsResponse) GetAlignments() []*Read { 1233 if x != nil { 1234 return x.Alignments 1235 } 1236 return nil 1237} 1238 1239var File_google_genomics_v1_reads_proto protoreflect.FileDescriptor 1240 1241var file_google_genomics_v1_reads_proto_rawDesc = []byte{ 1242 0x0a, 0x1e, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2f, 0x67, 0x65, 0x6e, 0x6f, 0x6d, 0x69, 0x63, 1243 0x73, 0x2f, 0x76, 0x31, 0x2f, 0x72, 0x65, 0x61, 0x64, 0x73, 0x2e, 0x70, 0x72, 0x6f, 0x74, 0x6f, 1244 0x12, 0x12, 0x67, 0x6f, 0x6f, 0x67, 0x6c, 0x65, 0x2e, 0x67, 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1518 file_google_genomics_v1_reads_proto_rawDescData = protoimpl.X.CompressGZIP(file_google_genomics_v1_reads_proto_rawDescData) 1519 }) 1520 return file_google_genomics_v1_reads_proto_rawDescData 1521} 1522 1523var file_google_genomics_v1_reads_proto_enumTypes = make([]protoimpl.EnumInfo, 1) 1524var file_google_genomics_v1_reads_proto_msgTypes = make([]protoimpl.MessageInfo, 15) 1525var file_google_genomics_v1_reads_proto_goTypes = []interface{}{ 1526 (ImportReadGroupSetsRequest_PartitionStrategy)(0), // 0: google.genomics.v1.ImportReadGroupSetsRequest.PartitionStrategy 1527 (*SearchReadGroupSetsRequest)(nil), // 1: google.genomics.v1.SearchReadGroupSetsRequest 1528 (*SearchReadGroupSetsResponse)(nil), // 2: google.genomics.v1.SearchReadGroupSetsResponse 1529 (*ImportReadGroupSetsRequest)(nil), // 3: google.genomics.v1.ImportReadGroupSetsRequest 1530 (*ImportReadGroupSetsResponse)(nil), // 4: google.genomics.v1.ImportReadGroupSetsResponse 1531 (*ExportReadGroupSetRequest)(nil), // 5: google.genomics.v1.ExportReadGroupSetRequest 1532 (*UpdateReadGroupSetRequest)(nil), // 6: google.genomics.v1.UpdateReadGroupSetRequest 1533 (*DeleteReadGroupSetRequest)(nil), // 7: google.genomics.v1.DeleteReadGroupSetRequest 1534 (*GetReadGroupSetRequest)(nil), // 8: google.genomics.v1.GetReadGroupSetRequest 1535 (*ListCoverageBucketsRequest)(nil), // 9: google.genomics.v1.ListCoverageBucketsRequest 1536 (*CoverageBucket)(nil), // 10: google.genomics.v1.CoverageBucket 1537 (*ListCoverageBucketsResponse)(nil), // 11: google.genomics.v1.ListCoverageBucketsResponse 1538 (*SearchReadsRequest)(nil), // 12: google.genomics.v1.SearchReadsRequest 1539 (*SearchReadsResponse)(nil), // 13: google.genomics.v1.SearchReadsResponse 1540 (*StreamReadsRequest)(nil), // 14: google.genomics.v1.StreamReadsRequest 1541 (*StreamReadsResponse)(nil), // 15: google.genomics.v1.StreamReadsResponse 1542 (*ReadGroupSet)(nil), // 16: google.genomics.v1.ReadGroupSet 1543 (*fieldmaskpb.FieldMask)(nil), // 17: google.protobuf.FieldMask 1544 (*Range)(nil), // 18: google.genomics.v1.Range 1545 (*Read)(nil), // 19: google.genomics.v1.Read 1546 (*longrunning.Operation)(nil), // 20: google.longrunning.Operation 1547 (*emptypb.Empty)(nil), // 21: google.protobuf.Empty 1548} 1549var file_google_genomics_v1_reads_proto_depIdxs = []int32{ 1550 16, // 0: google.genomics.v1.SearchReadGroupSetsResponse.read_group_sets:type_name -> google.genomics.v1.ReadGroupSet 1551 0, // 1: google.genomics.v1.ImportReadGroupSetsRequest.partition_strategy:type_name -> google.genomics.v1.ImportReadGroupSetsRequest.PartitionStrategy 1552 16, // 2: google.genomics.v1.UpdateReadGroupSetRequest.read_group_set:type_name -> google.genomics.v1.ReadGroupSet 1553 17, // 3: google.genomics.v1.UpdateReadGroupSetRequest.update_mask:type_name -> google.protobuf.FieldMask 1554 18, // 4: google.genomics.v1.CoverageBucket.range:type_name -> google.genomics.v1.Range 1555 10, // 5: google.genomics.v1.ListCoverageBucketsResponse.coverage_buckets:type_name -> google.genomics.v1.CoverageBucket 1556 19, // 6: google.genomics.v1.SearchReadsResponse.alignments:type_name -> google.genomics.v1.Read 1557 19, // 7: google.genomics.v1.StreamReadsResponse.alignments:type_name -> google.genomics.v1.Read 1558 14, // 8: google.genomics.v1.StreamingReadService.StreamReads:input_type -> google.genomics.v1.StreamReadsRequest 1559 3, // 9: google.genomics.v1.ReadServiceV1.ImportReadGroupSets:input_type -> google.genomics.v1.ImportReadGroupSetsRequest 1560 5, // 10: google.genomics.v1.ReadServiceV1.ExportReadGroupSet:input_type -> google.genomics.v1.ExportReadGroupSetRequest 1561 1, // 11: google.genomics.v1.ReadServiceV1.SearchReadGroupSets:input_type -> google.genomics.v1.SearchReadGroupSetsRequest 1562 6, // 12: google.genomics.v1.ReadServiceV1.UpdateReadGroupSet:input_type -> google.genomics.v1.UpdateReadGroupSetRequest 1563 7, // 13: google.genomics.v1.ReadServiceV1.DeleteReadGroupSet:input_type -> google.genomics.v1.DeleteReadGroupSetRequest 1564 8, // 14: google.genomics.v1.ReadServiceV1.GetReadGroupSet:input_type -> google.genomics.v1.GetReadGroupSetRequest 1565 9, // 15: google.genomics.v1.ReadServiceV1.ListCoverageBuckets:input_type -> google.genomics.v1.ListCoverageBucketsRequest 1566 12, // 16: google.genomics.v1.ReadServiceV1.SearchReads:input_type -> google.genomics.v1.SearchReadsRequest 1567 15, // 17: google.genomics.v1.StreamingReadService.StreamReads:output_type -> google.genomics.v1.StreamReadsResponse 1568 20, // 18: google.genomics.v1.ReadServiceV1.ImportReadGroupSets:output_type -> google.longrunning.Operation 1569 20, // 19: google.genomics.v1.ReadServiceV1.ExportReadGroupSet:output_type -> google.longrunning.Operation 1570 2, // 20: google.genomics.v1.ReadServiceV1.SearchReadGroupSets:output_type -> google.genomics.v1.SearchReadGroupSetsResponse 1571 16, // 21: google.genomics.v1.ReadServiceV1.UpdateReadGroupSet:output_type -> google.genomics.v1.ReadGroupSet 1572 21, // 22: google.genomics.v1.ReadServiceV1.DeleteReadGroupSet:output_type -> google.protobuf.Empty 1573 16, // 23: google.genomics.v1.ReadServiceV1.GetReadGroupSet:output_type -> google.genomics.v1.ReadGroupSet 1574 11, // 24: google.genomics.v1.ReadServiceV1.ListCoverageBuckets:output_type -> google.genomics.v1.ListCoverageBucketsResponse 1575 13, // 25: google.genomics.v1.ReadServiceV1.SearchReads:output_type -> google.genomics.v1.SearchReadsResponse 1576 17, // [17:26] is the sub-list for method output_type 1577 8, // [8:17] is the sub-list for method input_type 1578 8, // [8:8] is the sub-list for extension type_name 1579 8, // [8:8] is the sub-list for extension extendee 1580 0, // [0:8] is the sub-list for field type_name 1581} 1582 1583func init() { file_google_genomics_v1_reads_proto_init() } 1584func file_google_genomics_v1_reads_proto_init() { 1585 if File_google_genomics_v1_reads_proto != nil { 1586 return 1587 } 1588 file_google_genomics_v1_range_proto_init() 1589 file_google_genomics_v1_readalignment_proto_init() 1590 file_google_genomics_v1_readgroupset_proto_init() 1591 if !protoimpl.UnsafeEnabled { 1592 file_google_genomics_v1_reads_proto_msgTypes[0].Exporter = func(v interface{}, i int) interface{} { 1593 switch v := v.(*SearchReadGroupSetsRequest); i { 1594 case 0: 1595 return &v.state 1596 case 1: 1597 return &v.sizeCache 1598 case 2: 1599 return &v.unknownFields 1600 default: 1601 return nil 1602 } 1603 } 1604 file_google_genomics_v1_reads_proto_msgTypes[1].Exporter = func(v interface{}, i int) interface{} { 1605 switch v := v.(*SearchReadGroupSetsResponse); i { 1606 case 0: 1607 return &v.state 1608 case 1: 1609 return &v.sizeCache 1610 case 2: 1611 return &v.unknownFields 1612 default: 1613 return nil 1614 } 1615 } 1616 file_google_genomics_v1_reads_proto_msgTypes[2].Exporter = func(v interface{}, i int) interface{} { 1617 switch v := v.(*ImportReadGroupSetsRequest); i { 1618 case 0: 1619 return &v.state 1620 case 1: 1621 return &v.sizeCache 1622 case 2: 1623 return &v.unknownFields 1624 default: 1625 return nil 1626 } 1627 } 1628 file_google_genomics_v1_reads_proto_msgTypes[3].Exporter = func(v interface{}, i int) interface{} { 1629 switch v := v.(*ImportReadGroupSetsResponse); i { 1630 case 0: 1631 return &v.state 1632 case 1: 1633 return &v.sizeCache 1634 case 2: 1635 return &v.unknownFields 1636 default: 1637 return nil 1638 } 1639 } 1640 file_google_genomics_v1_reads_proto_msgTypes[4].Exporter = func(v interface{}, i int) interface{} { 1641 switch v := v.(*ExportReadGroupSetRequest); i { 1642 case 0: 1643 return &v.state 1644 case 1: 1645 return &v.sizeCache 1646 case 2: 1647 return &v.unknownFields 1648 default: 1649 return nil 1650 } 1651 } 1652 file_google_genomics_v1_reads_proto_msgTypes[5].Exporter = func(v interface{}, i int) interface{} { 1653 switch v := v.(*UpdateReadGroupSetRequest); i { 1654 case 0: 1655 return &v.state 1656 case 1: 1657 return &v.sizeCache 1658 case 2: 1659 return &v.unknownFields 1660 default: 1661 return nil 1662 } 1663 } 1664 file_google_genomics_v1_reads_proto_msgTypes[6].Exporter = func(v interface{}, i int) interface{} { 1665 switch v := v.(*DeleteReadGroupSetRequest); i { 1666 case 0: 1667 return &v.state 1668 case 1: 1669 return &v.sizeCache 1670 case 2: 1671 return &v.unknownFields 1672 default: 1673 return nil 1674 } 1675 } 1676 file_google_genomics_v1_reads_proto_msgTypes[7].Exporter = func(v interface{}, i int) interface{} { 1677 switch v := v.(*GetReadGroupSetRequest); i { 1678 case 0: 1679 return &v.state 1680 case 1: 1681 return &v.sizeCache 1682 case 2: 1683 return &v.unknownFields 1684 default: 1685 return nil 1686 } 1687 } 1688 file_google_genomics_v1_reads_proto_msgTypes[8].Exporter = func(v interface{}, i int) interface{} { 1689 switch v := v.(*ListCoverageBucketsRequest); i { 1690 case 0: 1691 return &v.state 1692 case 1: 1693 return &v.sizeCache 1694 case 2: 1695 return &v.unknownFields 1696 default: 1697 return nil 1698 } 1699 } 1700 file_google_genomics_v1_reads_proto_msgTypes[9].Exporter = func(v interface{}, i int) interface{} { 1701 switch v := v.(*CoverageBucket); i { 1702 case 0: 1703 return &v.state 1704 case 1: 1705 return &v.sizeCache 1706 case 2: 1707 return &v.unknownFields 1708 default: 1709 return nil 1710 } 1711 } 1712 file_google_genomics_v1_reads_proto_msgTypes[10].Exporter = func(v interface{}, i int) interface{} { 1713 switch v := v.(*ListCoverageBucketsResponse); i { 1714 case 0: 1715 return &v.state 1716 case 1: 1717 return &v.sizeCache 1718 case 2: 1719 return &v.unknownFields 1720 default: 1721 return nil 1722 } 1723 } 1724 file_google_genomics_v1_reads_proto_msgTypes[11].Exporter = func(v interface{}, i int) interface{} { 1725 switch v := v.(*SearchReadsRequest); i { 1726 case 0: 1727 return &v.state 1728 case 1: 1729 return &v.sizeCache 1730 case 2: 1731 return &v.unknownFields 1732 default: 1733 return nil 1734 } 1735 } 1736 file_google_genomics_v1_reads_proto_msgTypes[12].Exporter = func(v interface{}, i int) interface{} { 1737 switch v := v.(*SearchReadsResponse); i { 1738 case 0: 1739 return &v.state 1740 case 1: 1741 return &v.sizeCache 1742 case 2: 1743 return &v.unknownFields 1744 default: 1745 return nil 1746 } 1747 } 1748 file_google_genomics_v1_reads_proto_msgTypes[13].Exporter = func(v interface{}, i int) interface{} { 1749 switch v := v.(*StreamReadsRequest); i { 1750 case 0: 1751 return &v.state 1752 case 1: 1753 return &v.sizeCache 1754 case 2: 1755 return &v.unknownFields 1756 default: 1757 return nil 1758 } 1759 } 1760 file_google_genomics_v1_reads_proto_msgTypes[14].Exporter = func(v interface{}, i int) interface{} { 1761 switch v := v.(*StreamReadsResponse); i { 1762 case 0: 1763 return &v.state 1764 case 1: 1765 return &v.sizeCache 1766 case 2: 1767 return &v.unknownFields 1768 default: 1769 return nil 1770 } 1771 } 1772 } 1773 type x struct{} 1774 out := protoimpl.TypeBuilder{ 1775 File: protoimpl.DescBuilder{ 1776 GoPackagePath: reflect.TypeOf(x{}).PkgPath(), 1777 RawDescriptor: file_google_genomics_v1_reads_proto_rawDesc, 1778 NumEnums: 1, 1779 NumMessages: 15, 1780 NumExtensions: 0, 1781 NumServices: 2, 1782 }, 1783 GoTypes: file_google_genomics_v1_reads_proto_goTypes, 1784 DependencyIndexes: file_google_genomics_v1_reads_proto_depIdxs, 1785 EnumInfos: file_google_genomics_v1_reads_proto_enumTypes, 1786 MessageInfos: file_google_genomics_v1_reads_proto_msgTypes, 1787 }.Build() 1788 File_google_genomics_v1_reads_proto = out.File 1789 file_google_genomics_v1_reads_proto_rawDesc = nil 1790 file_google_genomics_v1_reads_proto_goTypes = nil 1791 file_google_genomics_v1_reads_proto_depIdxs = nil 1792} 1793 1794// Reference imports to suppress errors if they are not otherwise used. 1795var _ context.Context 1796var _ grpc.ClientConnInterface 1797 1798// This is a compile-time assertion to ensure that this generated file 1799// is compatible with the grpc package it is being compiled against. 1800const _ = grpc.SupportPackageIsVersion6 1801 1802// StreamingReadServiceClient is the client API for StreamingReadService service. 1803// 1804// For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream. 1805type StreamingReadServiceClient interface { 1806 // Returns a stream of all the reads matching the search request, ordered 1807 // by reference name, position, and ID. 1808 StreamReads(ctx context.Context, in *StreamReadsRequest, opts ...grpc.CallOption) (StreamingReadService_StreamReadsClient, error) 1809} 1810 1811type streamingReadServiceClient struct { 1812 cc grpc.ClientConnInterface 1813} 1814 1815func NewStreamingReadServiceClient(cc grpc.ClientConnInterface) StreamingReadServiceClient { 1816 return &streamingReadServiceClient{cc} 1817} 1818 1819func (c *streamingReadServiceClient) StreamReads(ctx context.Context, in *StreamReadsRequest, opts ...grpc.CallOption) (StreamingReadService_StreamReadsClient, error) { 1820 stream, err := c.cc.NewStream(ctx, &_StreamingReadService_serviceDesc.Streams[0], "/google.genomics.v1.StreamingReadService/StreamReads", opts...) 1821 if err != nil { 1822 return nil, err 1823 } 1824 x := &streamingReadServiceStreamReadsClient{stream} 1825 if err := x.ClientStream.SendMsg(in); err != nil { 1826 return nil, err 1827 } 1828 if err := x.ClientStream.CloseSend(); err != nil { 1829 return nil, err 1830 } 1831 return x, nil 1832} 1833 1834type StreamingReadService_StreamReadsClient interface { 1835 Recv() (*StreamReadsResponse, error) 1836 grpc.ClientStream 1837} 1838 1839type streamingReadServiceStreamReadsClient struct { 1840 grpc.ClientStream 1841} 1842 1843func (x *streamingReadServiceStreamReadsClient) Recv() (*StreamReadsResponse, error) { 1844 m := new(StreamReadsResponse) 1845 if err := x.ClientStream.RecvMsg(m); err != nil { 1846 return nil, err 1847 } 1848 return m, nil 1849} 1850 1851// StreamingReadServiceServer is the server API for StreamingReadService service. 1852type StreamingReadServiceServer interface { 1853 // Returns a stream of all the reads matching the search request, ordered 1854 // by reference name, position, and ID. 1855 StreamReads(*StreamReadsRequest, StreamingReadService_StreamReadsServer) error 1856} 1857 1858// UnimplementedStreamingReadServiceServer can be embedded to have forward compatible implementations. 1859type UnimplementedStreamingReadServiceServer struct { 1860} 1861 1862func (*UnimplementedStreamingReadServiceServer) StreamReads(*StreamReadsRequest, StreamingReadService_StreamReadsServer) error { 1863 return status.Errorf(codes.Unimplemented, "method StreamReads not implemented") 1864} 1865 1866func RegisterStreamingReadServiceServer(s *grpc.Server, srv StreamingReadServiceServer) { 1867 s.RegisterService(&_StreamingReadService_serviceDesc, srv) 1868} 1869 1870func _StreamingReadService_StreamReads_Handler(srv interface{}, stream grpc.ServerStream) error { 1871 m := new(StreamReadsRequest) 1872 if err := stream.RecvMsg(m); err != nil { 1873 return err 1874 } 1875 return srv.(StreamingReadServiceServer).StreamReads(m, &streamingReadServiceStreamReadsServer{stream}) 1876} 1877 1878type StreamingReadService_StreamReadsServer interface { 1879 Send(*StreamReadsResponse) error 1880 grpc.ServerStream 1881} 1882 1883type streamingReadServiceStreamReadsServer struct { 1884 grpc.ServerStream 1885} 1886 1887func (x *streamingReadServiceStreamReadsServer) Send(m *StreamReadsResponse) error { 1888 return x.ServerStream.SendMsg(m) 1889} 1890 1891var _StreamingReadService_serviceDesc = grpc.ServiceDesc{ 1892 ServiceName: "google.genomics.v1.StreamingReadService", 1893 HandlerType: (*StreamingReadServiceServer)(nil), 1894 Methods: []grpc.MethodDesc{}, 1895 Streams: []grpc.StreamDesc{ 1896 { 1897 StreamName: "StreamReads", 1898 Handler: _StreamingReadService_StreamReads_Handler, 1899 ServerStreams: true, 1900 }, 1901 }, 1902 Metadata: "google/genomics/v1/reads.proto", 1903} 1904 1905// ReadServiceV1Client is the client API for ReadServiceV1 service. 1906// 1907// For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream. 1908type ReadServiceV1Client interface { 1909 // Creates read group sets by asynchronously importing the provided 1910 // information. 1911 // 1912 // For the definitions of read group sets and other genomics resources, see 1913 // [Fundamentals of Google 1914 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1915 // 1916 // The caller must have WRITE permissions to the dataset. 1917 // 1918 // ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import 1919 // 1920 // - Tags will be converted to strings - tag types are not preserved 1921 // - Comments (`@CO`) in the input file header will not be preserved 1922 // - Original header order of references (`@SQ`) will not be preserved 1923 // - Any reverse stranded unmapped reads will be reverse complemented, and 1924 // their qualities (also the "BQ" and "OQ" tags, if any) will be reversed 1925 // - Unmapped reads will be stripped of positional information (reference name 1926 // and position) 1927 ImportReadGroupSets(ctx context.Context, in *ImportReadGroupSetsRequest, opts ...grpc.CallOption) (*longrunning.Operation, error) 1928 // Exports a read group set to a BAM file in Google Cloud Storage. 1929 // 1930 // For the definitions of read group sets and other genomics resources, see 1931 // [Fundamentals of Google 1932 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1933 // 1934 // Note that currently there may be some differences between exported BAM 1935 // files and the original BAM file at the time of import. See 1936 // [ImportReadGroupSets][google.genomics.v1.ReadServiceV1.ImportReadGroupSets] 1937 // for caveats. 1938 ExportReadGroupSet(ctx context.Context, in *ExportReadGroupSetRequest, opts ...grpc.CallOption) (*longrunning.Operation, error) 1939 // Searches for read group sets matching the criteria. 1940 // 1941 // For the definitions of read group sets and other genomics resources, see 1942 // [Fundamentals of Google 1943 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1944 // 1945 // Implements 1946 // [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). 1947 SearchReadGroupSets(ctx context.Context, in *SearchReadGroupSetsRequest, opts ...grpc.CallOption) (*SearchReadGroupSetsResponse, error) 1948 // Updates a read group set. 1949 // 1950 // For the definitions of read group sets and other genomics resources, see 1951 // [Fundamentals of Google 1952 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1953 // 1954 // This method supports patch semantics. 1955 UpdateReadGroupSet(ctx context.Context, in *UpdateReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error) 1956 // Deletes a read group set. 1957 // 1958 // For the definitions of read group sets and other genomics resources, see 1959 // [Fundamentals of Google 1960 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1961 DeleteReadGroupSet(ctx context.Context, in *DeleteReadGroupSetRequest, opts ...grpc.CallOption) (*emptypb.Empty, error) 1962 // Gets a read group set by ID. 1963 // 1964 // For the definitions of read group sets and other genomics resources, see 1965 // [Fundamentals of Google 1966 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1967 GetReadGroupSet(ctx context.Context, in *GetReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error) 1968 // Lists fixed width coverage buckets for a read group set, each of which 1969 // correspond to a range of a reference sequence. Each bucket summarizes 1970 // coverage information across its corresponding genomic range. 1971 // 1972 // For the definitions of read group sets and other genomics resources, see 1973 // [Fundamentals of Google 1974 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1975 // 1976 // Coverage is defined as the number of reads which are aligned to a given 1977 // base in the reference sequence. Coverage buckets are available at several 1978 // precomputed bucket widths, enabling retrieval of various coverage 'zoom 1979 // levels'. The caller must have READ permissions for the target read group 1980 // set. 1981 ListCoverageBuckets(ctx context.Context, in *ListCoverageBucketsRequest, opts ...grpc.CallOption) (*ListCoverageBucketsResponse, error) 1982 // Gets a list of reads for one or more read group sets. 1983 // 1984 // For the definitions of read group sets and other genomics resources, see 1985 // [Fundamentals of Google 1986 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 1987 // 1988 // Reads search operates over a genomic coordinate space of reference sequence 1989 // & position defined over the reference sequences to which the requested 1990 // read group sets are aligned. 1991 // 1992 // If a target positional range is specified, search returns all reads whose 1993 // alignment to the reference genome overlap the range. A query which 1994 // specifies only read group set IDs yields all reads in those read group 1995 // sets, including unmapped reads. 1996 // 1997 // All reads returned (including reads on subsequent pages) are ordered by 1998 // genomic coordinate (by reference sequence, then position). Reads with 1999 // equivalent genomic coordinates are returned in an unspecified order. This 2000 // order is consistent, such that two queries for the same content (regardless 2001 // of page size) yield reads in the same order across their respective streams 2002 // of paginated responses. 2003 // 2004 // Implements 2005 // [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85). 2006 SearchReads(ctx context.Context, in *SearchReadsRequest, opts ...grpc.CallOption) (*SearchReadsResponse, error) 2007} 2008 2009type readServiceV1Client struct { 2010 cc grpc.ClientConnInterface 2011} 2012 2013func NewReadServiceV1Client(cc grpc.ClientConnInterface) ReadServiceV1Client { 2014 return &readServiceV1Client{cc} 2015} 2016 2017func (c *readServiceV1Client) ImportReadGroupSets(ctx context.Context, in *ImportReadGroupSetsRequest, opts ...grpc.CallOption) (*longrunning.Operation, error) { 2018 out := new(longrunning.Operation) 2019 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/ImportReadGroupSets", in, out, opts...) 2020 if err != nil { 2021 return nil, err 2022 } 2023 return out, nil 2024} 2025 2026func (c *readServiceV1Client) ExportReadGroupSet(ctx context.Context, in *ExportReadGroupSetRequest, opts ...grpc.CallOption) (*longrunning.Operation, error) { 2027 out := new(longrunning.Operation) 2028 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/ExportReadGroupSet", in, out, opts...) 2029 if err != nil { 2030 return nil, err 2031 } 2032 return out, nil 2033} 2034 2035func (c *readServiceV1Client) SearchReadGroupSets(ctx context.Context, in *SearchReadGroupSetsRequest, opts ...grpc.CallOption) (*SearchReadGroupSetsResponse, error) { 2036 out := new(SearchReadGroupSetsResponse) 2037 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/SearchReadGroupSets", in, out, opts...) 2038 if err != nil { 2039 return nil, err 2040 } 2041 return out, nil 2042} 2043 2044func (c *readServiceV1Client) UpdateReadGroupSet(ctx context.Context, in *UpdateReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error) { 2045 out := new(ReadGroupSet) 2046 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/UpdateReadGroupSet", in, out, opts...) 2047 if err != nil { 2048 return nil, err 2049 } 2050 return out, nil 2051} 2052 2053func (c *readServiceV1Client) DeleteReadGroupSet(ctx context.Context, in *DeleteReadGroupSetRequest, opts ...grpc.CallOption) (*emptypb.Empty, error) { 2054 out := new(emptypb.Empty) 2055 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/DeleteReadGroupSet", in, out, opts...) 2056 if err != nil { 2057 return nil, err 2058 } 2059 return out, nil 2060} 2061 2062func (c *readServiceV1Client) GetReadGroupSet(ctx context.Context, in *GetReadGroupSetRequest, opts ...grpc.CallOption) (*ReadGroupSet, error) { 2063 out := new(ReadGroupSet) 2064 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/GetReadGroupSet", in, out, opts...) 2065 if err != nil { 2066 return nil, err 2067 } 2068 return out, nil 2069} 2070 2071func (c *readServiceV1Client) ListCoverageBuckets(ctx context.Context, in *ListCoverageBucketsRequest, opts ...grpc.CallOption) (*ListCoverageBucketsResponse, error) { 2072 out := new(ListCoverageBucketsResponse) 2073 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/ListCoverageBuckets", in, out, opts...) 2074 if err != nil { 2075 return nil, err 2076 } 2077 return out, nil 2078} 2079 2080func (c *readServiceV1Client) SearchReads(ctx context.Context, in *SearchReadsRequest, opts ...grpc.CallOption) (*SearchReadsResponse, error) { 2081 out := new(SearchReadsResponse) 2082 err := c.cc.Invoke(ctx, "/google.genomics.v1.ReadServiceV1/SearchReads", in, out, opts...) 2083 if err != nil { 2084 return nil, err 2085 } 2086 return out, nil 2087} 2088 2089// ReadServiceV1Server is the server API for ReadServiceV1 service. 2090type ReadServiceV1Server interface { 2091 // Creates read group sets by asynchronously importing the provided 2092 // information. 2093 // 2094 // For the definitions of read group sets and other genomics resources, see 2095 // [Fundamentals of Google 2096 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2097 // 2098 // The caller must have WRITE permissions to the dataset. 2099 // 2100 // ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import 2101 // 2102 // - Tags will be converted to strings - tag types are not preserved 2103 // - Comments (`@CO`) in the input file header will not be preserved 2104 // - Original header order of references (`@SQ`) will not be preserved 2105 // - Any reverse stranded unmapped reads will be reverse complemented, and 2106 // their qualities (also the "BQ" and "OQ" tags, if any) will be reversed 2107 // - Unmapped reads will be stripped of positional information (reference name 2108 // and position) 2109 ImportReadGroupSets(context.Context, *ImportReadGroupSetsRequest) (*longrunning.Operation, error) 2110 // Exports a read group set to a BAM file in Google Cloud Storage. 2111 // 2112 // For the definitions of read group sets and other genomics resources, see 2113 // [Fundamentals of Google 2114 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2115 // 2116 // Note that currently there may be some differences between exported BAM 2117 // files and the original BAM file at the time of import. See 2118 // [ImportReadGroupSets][google.genomics.v1.ReadServiceV1.ImportReadGroupSets] 2119 // for caveats. 2120 ExportReadGroupSet(context.Context, *ExportReadGroupSetRequest) (*longrunning.Operation, error) 2121 // Searches for read group sets matching the criteria. 2122 // 2123 // For the definitions of read group sets and other genomics resources, see 2124 // [Fundamentals of Google 2125 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2126 // 2127 // Implements 2128 // [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). 2129 SearchReadGroupSets(context.Context, *SearchReadGroupSetsRequest) (*SearchReadGroupSetsResponse, error) 2130 // Updates a read group set. 2131 // 2132 // For the definitions of read group sets and other genomics resources, see 2133 // [Fundamentals of Google 2134 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2135 // 2136 // This method supports patch semantics. 2137 UpdateReadGroupSet(context.Context, *UpdateReadGroupSetRequest) (*ReadGroupSet, error) 2138 // Deletes a read group set. 2139 // 2140 // For the definitions of read group sets and other genomics resources, see 2141 // [Fundamentals of Google 2142 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2143 DeleteReadGroupSet(context.Context, *DeleteReadGroupSetRequest) (*emptypb.Empty, error) 2144 // Gets a read group set by ID. 2145 // 2146 // For the definitions of read group sets and other genomics resources, see 2147 // [Fundamentals of Google 2148 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2149 GetReadGroupSet(context.Context, *GetReadGroupSetRequest) (*ReadGroupSet, error) 2150 // Lists fixed width coverage buckets for a read group set, each of which 2151 // correspond to a range of a reference sequence. Each bucket summarizes 2152 // coverage information across its corresponding genomic range. 2153 // 2154 // For the definitions of read group sets and other genomics resources, see 2155 // [Fundamentals of Google 2156 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2157 // 2158 // Coverage is defined as the number of reads which are aligned to a given 2159 // base in the reference sequence. Coverage buckets are available at several 2160 // precomputed bucket widths, enabling retrieval of various coverage 'zoom 2161 // levels'. The caller must have READ permissions for the target read group 2162 // set. 2163 ListCoverageBuckets(context.Context, *ListCoverageBucketsRequest) (*ListCoverageBucketsResponse, error) 2164 // Gets a list of reads for one or more read group sets. 2165 // 2166 // For the definitions of read group sets and other genomics resources, see 2167 // [Fundamentals of Google 2168 // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 2169 // 2170 // Reads search operates over a genomic coordinate space of reference sequence 2171 // & position defined over the reference sequences to which the requested 2172 // read group sets are aligned. 2173 // 2174 // If a target positional range is specified, search returns all reads whose 2175 // alignment to the reference genome overlap the range. A query which 2176 // specifies only read group set IDs yields all reads in those read group 2177 // sets, including unmapped reads. 2178 // 2179 // All reads returned (including reads on subsequent pages) are ordered by 2180 // genomic coordinate (by reference sequence, then position). Reads with 2181 // equivalent genomic coordinates are returned in an unspecified order. This 2182 // order is consistent, such that two queries for the same content (regardless 2183 // of page size) yield reads in the same order across their respective streams 2184 // of paginated responses. 2185 // 2186 // Implements 2187 // [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85). 2188 SearchReads(context.Context, *SearchReadsRequest) (*SearchReadsResponse, error) 2189} 2190 2191// UnimplementedReadServiceV1Server can be embedded to have forward compatible implementations. 2192type UnimplementedReadServiceV1Server struct { 2193} 2194 2195func (*UnimplementedReadServiceV1Server) ImportReadGroupSets(context.Context, *ImportReadGroupSetsRequest) (*longrunning.Operation, error) { 2196 return nil, status.Errorf(codes.Unimplemented, "method ImportReadGroupSets not implemented") 2197} 2198func (*UnimplementedReadServiceV1Server) ExportReadGroupSet(context.Context, *ExportReadGroupSetRequest) (*longrunning.Operation, error) { 2199 return nil, status.Errorf(codes.Unimplemented, "method ExportReadGroupSet not implemented") 2200} 2201func (*UnimplementedReadServiceV1Server) SearchReadGroupSets(context.Context, *SearchReadGroupSetsRequest) (*SearchReadGroupSetsResponse, error) { 2202 return nil, status.Errorf(codes.Unimplemented, "method SearchReadGroupSets not implemented") 2203} 2204func (*UnimplementedReadServiceV1Server) UpdateReadGroupSet(context.Context, *UpdateReadGroupSetRequest) (*ReadGroupSet, error) { 2205 return nil, status.Errorf(codes.Unimplemented, "method UpdateReadGroupSet not implemented") 2206} 2207func (*UnimplementedReadServiceV1Server) DeleteReadGroupSet(context.Context, *DeleteReadGroupSetRequest) (*emptypb.Empty, error) { 2208 return nil, status.Errorf(codes.Unimplemented, "method DeleteReadGroupSet not implemented") 2209} 2210func (*UnimplementedReadServiceV1Server) GetReadGroupSet(context.Context, *GetReadGroupSetRequest) (*ReadGroupSet, error) { 2211 return nil, status.Errorf(codes.Unimplemented, "method GetReadGroupSet not implemented") 2212} 2213func (*UnimplementedReadServiceV1Server) ListCoverageBuckets(context.Context, *ListCoverageBucketsRequest) (*ListCoverageBucketsResponse, error) { 2214 return nil, status.Errorf(codes.Unimplemented, "method ListCoverageBuckets not implemented") 2215} 2216func (*UnimplementedReadServiceV1Server) SearchReads(context.Context, *SearchReadsRequest) (*SearchReadsResponse, error) { 2217 return nil, status.Errorf(codes.Unimplemented, "method SearchReads not implemented") 2218} 2219 2220func RegisterReadServiceV1Server(s *grpc.Server, srv ReadServiceV1Server) { 2221 s.RegisterService(&_ReadServiceV1_serviceDesc, srv) 2222} 2223 2224func _ReadServiceV1_ImportReadGroupSets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2225 in := new(ImportReadGroupSetsRequest) 2226 if err := dec(in); err != nil { 2227 return nil, err 2228 } 2229 if interceptor == nil { 2230 return srv.(ReadServiceV1Server).ImportReadGroupSets(ctx, in) 2231 } 2232 info := &grpc.UnaryServerInfo{ 2233 Server: srv, 2234 FullMethod: "/google.genomics.v1.ReadServiceV1/ImportReadGroupSets", 2235 } 2236 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2237 return srv.(ReadServiceV1Server).ImportReadGroupSets(ctx, req.(*ImportReadGroupSetsRequest)) 2238 } 2239 return interceptor(ctx, in, info, handler) 2240} 2241 2242func _ReadServiceV1_ExportReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2243 in := new(ExportReadGroupSetRequest) 2244 if err := dec(in); err != nil { 2245 return nil, err 2246 } 2247 if interceptor == nil { 2248 return srv.(ReadServiceV1Server).ExportReadGroupSet(ctx, in) 2249 } 2250 info := &grpc.UnaryServerInfo{ 2251 Server: srv, 2252 FullMethod: "/google.genomics.v1.ReadServiceV1/ExportReadGroupSet", 2253 } 2254 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2255 return srv.(ReadServiceV1Server).ExportReadGroupSet(ctx, req.(*ExportReadGroupSetRequest)) 2256 } 2257 return interceptor(ctx, in, info, handler) 2258} 2259 2260func _ReadServiceV1_SearchReadGroupSets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2261 in := new(SearchReadGroupSetsRequest) 2262 if err := dec(in); err != nil { 2263 return nil, err 2264 } 2265 if interceptor == nil { 2266 return srv.(ReadServiceV1Server).SearchReadGroupSets(ctx, in) 2267 } 2268 info := &grpc.UnaryServerInfo{ 2269 Server: srv, 2270 FullMethod: "/google.genomics.v1.ReadServiceV1/SearchReadGroupSets", 2271 } 2272 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2273 return srv.(ReadServiceV1Server).SearchReadGroupSets(ctx, req.(*SearchReadGroupSetsRequest)) 2274 } 2275 return interceptor(ctx, in, info, handler) 2276} 2277 2278func _ReadServiceV1_UpdateReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2279 in := new(UpdateReadGroupSetRequest) 2280 if err := dec(in); err != nil { 2281 return nil, err 2282 } 2283 if interceptor == nil { 2284 return srv.(ReadServiceV1Server).UpdateReadGroupSet(ctx, in) 2285 } 2286 info := &grpc.UnaryServerInfo{ 2287 Server: srv, 2288 FullMethod: "/google.genomics.v1.ReadServiceV1/UpdateReadGroupSet", 2289 } 2290 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2291 return srv.(ReadServiceV1Server).UpdateReadGroupSet(ctx, req.(*UpdateReadGroupSetRequest)) 2292 } 2293 return interceptor(ctx, in, info, handler) 2294} 2295 2296func _ReadServiceV1_DeleteReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2297 in := new(DeleteReadGroupSetRequest) 2298 if err := dec(in); err != nil { 2299 return nil, err 2300 } 2301 if interceptor == nil { 2302 return srv.(ReadServiceV1Server).DeleteReadGroupSet(ctx, in) 2303 } 2304 info := &grpc.UnaryServerInfo{ 2305 Server: srv, 2306 FullMethod: "/google.genomics.v1.ReadServiceV1/DeleteReadGroupSet", 2307 } 2308 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2309 return srv.(ReadServiceV1Server).DeleteReadGroupSet(ctx, req.(*DeleteReadGroupSetRequest)) 2310 } 2311 return interceptor(ctx, in, info, handler) 2312} 2313 2314func _ReadServiceV1_GetReadGroupSet_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2315 in := new(GetReadGroupSetRequest) 2316 if err := dec(in); err != nil { 2317 return nil, err 2318 } 2319 if interceptor == nil { 2320 return srv.(ReadServiceV1Server).GetReadGroupSet(ctx, in) 2321 } 2322 info := &grpc.UnaryServerInfo{ 2323 Server: srv, 2324 FullMethod: "/google.genomics.v1.ReadServiceV1/GetReadGroupSet", 2325 } 2326 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2327 return srv.(ReadServiceV1Server).GetReadGroupSet(ctx, req.(*GetReadGroupSetRequest)) 2328 } 2329 return interceptor(ctx, in, info, handler) 2330} 2331 2332func _ReadServiceV1_ListCoverageBuckets_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2333 in := new(ListCoverageBucketsRequest) 2334 if err := dec(in); err != nil { 2335 return nil, err 2336 } 2337 if interceptor == nil { 2338 return srv.(ReadServiceV1Server).ListCoverageBuckets(ctx, in) 2339 } 2340 info := &grpc.UnaryServerInfo{ 2341 Server: srv, 2342 FullMethod: "/google.genomics.v1.ReadServiceV1/ListCoverageBuckets", 2343 } 2344 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2345 return srv.(ReadServiceV1Server).ListCoverageBuckets(ctx, req.(*ListCoverageBucketsRequest)) 2346 } 2347 return interceptor(ctx, in, info, handler) 2348} 2349 2350func _ReadServiceV1_SearchReads_Handler(srv interface{}, ctx context.Context, dec func(interface{}) error, interceptor grpc.UnaryServerInterceptor) (interface{}, error) { 2351 in := new(SearchReadsRequest) 2352 if err := dec(in); err != nil { 2353 return nil, err 2354 } 2355 if interceptor == nil { 2356 return srv.(ReadServiceV1Server).SearchReads(ctx, in) 2357 } 2358 info := &grpc.UnaryServerInfo{ 2359 Server: srv, 2360 FullMethod: "/google.genomics.v1.ReadServiceV1/SearchReads", 2361 } 2362 handler := func(ctx context.Context, req interface{}) (interface{}, error) { 2363 return srv.(ReadServiceV1Server).SearchReads(ctx, req.(*SearchReadsRequest)) 2364 } 2365 return interceptor(ctx, in, info, handler) 2366} 2367 2368var _ReadServiceV1_serviceDesc = grpc.ServiceDesc{ 2369 ServiceName: "google.genomics.v1.ReadServiceV1", 2370 HandlerType: (*ReadServiceV1Server)(nil), 2371 Methods: []grpc.MethodDesc{ 2372 { 2373 MethodName: "ImportReadGroupSets", 2374 Handler: _ReadServiceV1_ImportReadGroupSets_Handler, 2375 }, 2376 { 2377 MethodName: "ExportReadGroupSet", 2378 Handler: _ReadServiceV1_ExportReadGroupSet_Handler, 2379 }, 2380 { 2381 MethodName: "SearchReadGroupSets", 2382 Handler: _ReadServiceV1_SearchReadGroupSets_Handler, 2383 }, 2384 { 2385 MethodName: "UpdateReadGroupSet", 2386 Handler: _ReadServiceV1_UpdateReadGroupSet_Handler, 2387 }, 2388 { 2389 MethodName: "DeleteReadGroupSet", 2390 Handler: _ReadServiceV1_DeleteReadGroupSet_Handler, 2391 }, 2392 { 2393 MethodName: "GetReadGroupSet", 2394 Handler: _ReadServiceV1_GetReadGroupSet_Handler, 2395 }, 2396 { 2397 MethodName: "ListCoverageBuckets", 2398 Handler: _ReadServiceV1_ListCoverageBuckets_Handler, 2399 }, 2400 { 2401 MethodName: "SearchReads", 2402 Handler: _ReadServiceV1_SearchReads_Handler, 2403 }, 2404 }, 2405 Streams: []grpc.StreamDesc{}, 2406 Metadata: "google/genomics/v1/reads.proto", 2407} 2408