1<html><body> 2<style> 3 4body, h1, h2, h3, div, span, p, pre, a { 5 margin: 0; 6 padding: 0; 7 border: 0; 8 font-weight: inherit; 9 font-style: inherit; 10 font-size: 100%; 11 font-family: inherit; 12 vertical-align: baseline; 13} 14 15body { 16 font-size: 13px; 17 padding: 1em; 18} 19 20h1 { 21 font-size: 26px; 22 margin-bottom: 1em; 23} 24 25h2 { 26 font-size: 24px; 27 margin-bottom: 1em; 28} 29 30h3 { 31 font-size: 20px; 32 margin-bottom: 1em; 33 margin-top: 1em; 34} 35 36pre, code { 37 line-height: 1.5; 38 font-family: Monaco, 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', 'Lucida Console', monospace; 39} 40 41pre { 42 margin-top: 0.5em; 43} 44 45h1, h2, h3, p { 46 font-family: Arial, sans serif; 47} 48 49h1, h2, h3 { 50 border-bottom: solid #CCC 1px; 51} 52 53.toc_element { 54 margin-top: 0.5em; 55} 56 57.firstline { 58 margin-left: 2 em; 59} 60 61.method { 62 margin-top: 1em; 63 border: solid 1px #CCC; 64 padding: 1em; 65 background: #EEE; 66} 67 68.details { 69 font-weight: bold; 70 font-size: 14px; 71} 72 73</style> 74 75<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.readgroupsets.html">readgroupsets</a></h1> 76<h2>Instance Methods</h2> 77<p class="toc_element"> 78 <code><a href="genomics_v1.readgroupsets.coveragebuckets.html">coveragebuckets()</a></code> 79</p> 80<p class="firstline">Returns the coveragebuckets Resource.</p> 81 82<p class="toc_element"> 83 <code><a href="#delete">delete(readGroupSetId, x__xgafv=None)</a></code></p> 84<p class="firstline">Deletes a read group set.</p> 85<p class="toc_element"> 86 <code><a href="#export">export(readGroupSetId, body, x__xgafv=None)</a></code></p> 87<p class="firstline">Exports a read group set to a BAM file in Google Cloud Storage.</p> 88<p class="toc_element"> 89 <code><a href="#get">get(readGroupSetId, x__xgafv=None)</a></code></p> 90<p class="firstline">Gets a read group set by ID.</p> 91<p class="toc_element"> 92 <code><a href="#import_">import_(body, x__xgafv=None)</a></code></p> 93<p class="firstline">Creates read group sets by asynchronously importing the provided</p> 94<p class="toc_element"> 95 <code><a href="#patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</a></code></p> 96<p class="firstline">Updates a read group set.</p> 97<p class="toc_element"> 98 <code><a href="#search">search(body, x__xgafv=None)</a></code></p> 99<p class="firstline">Searches for read group sets matching the criteria.</p> 100<p class="toc_element"> 101 <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> 102<p class="firstline">Retrieves the next page of results.</p> 103<h3>Method Details</h3> 104<div class="method"> 105 <code class="details" id="delete">delete(readGroupSetId, x__xgafv=None)</code> 106 <pre>Deletes a read group set. 107 108For the definitions of read group sets and other genomics resources, see 109[Fundamentals of Google 110Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 111 112Args: 113 readGroupSetId: string, The ID of the read group set to be deleted. The caller must have WRITE 114permissions to the dataset associated with this read group set. (required) 115 x__xgafv: string, V1 error format. 116 Allowed values 117 1 - v1 error format 118 2 - v2 error format 119 120Returns: 121 An object of the form: 122 123 { # A generic empty message that you can re-use to avoid defining duplicated 124 # empty messages in your APIs. A typical example is to use it as the request 125 # or the response type of an API method. For instance: 126 # 127 # service Foo { 128 # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); 129 # } 130 # 131 # The JSON representation for `Empty` is empty JSON object `{}`. 132 }</pre> 133</div> 134 135<div class="method"> 136 <code class="details" id="export">export(readGroupSetId, body, x__xgafv=None)</code> 137 <pre>Exports a read group set to a BAM file in Google Cloud Storage. 138 139For the definitions of read group sets and other genomics resources, see 140[Fundamentals of Google 141Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 142 143Note that currently there may be some differences between exported BAM 144files and the original BAM file at the time of import. See 145ImportReadGroupSets 146for caveats. 147 148Args: 149 readGroupSetId: string, Required. The ID of the read group set to export. The caller must have 150READ access to this read group set. (required) 151 body: object, The request body. (required) 152 The object takes the form of: 153 154{ # The read group set export request. 155 "projectId": "A String", # Required. The Google Cloud project ID that owns this 156 # export. The caller must have WRITE access to this project. 157 "referenceNames": [ # The reference names to export. If this is not specified, all reference 158 # sequences, including unmapped reads, are exported. 159 # Use `*` to export only unmapped reads. 160 "A String", 161 ], 162 "exportUri": "A String", # Required. A Google Cloud Storage URI for the exported BAM file. 163 # The currently authenticated user must have write access to the new file. 164 # An error will be returned if the URI already contains data. 165 } 166 167 x__xgafv: string, V1 error format. 168 Allowed values 169 1 - v1 error format 170 2 - v2 error format 171 172Returns: 173 An object of the form: 174 175 { # This resource represents a long-running operation that is the result of a 176 # network API call. 177 "metadata": { # An OperationMetadata object. This will always be returned with the Operation. 178 "a_key": "", # Properties of the object. Contains field @type with type URL. 179 }, 180 "error": { # The `Status` type defines a logical error model that is suitable for different # The error result of the operation in case of failure or cancellation. 181 # programming environments, including REST APIs and RPC APIs. It is used by 182 # [gRPC](https://github.com/grpc). The error model is designed to be: 183 # 184 # - Simple to use and understand for most users 185 # - Flexible enough to meet unexpected needs 186 # 187 # # Overview 188 # 189 # The `Status` message contains three pieces of data: error code, error message, 190 # and error details. The error code should be an enum value of 191 # google.rpc.Code, but it may accept additional error codes if needed. The 192 # error message should be a developer-facing English message that helps 193 # developers *understand* and *resolve* the error. If a localized user-facing 194 # error message is needed, put the localized message in the error details or 195 # localize it in the client. The optional error details may contain arbitrary 196 # information about the error. There is a predefined set of error detail types 197 # in the package `google.rpc` that can be used for common error conditions. 198 # 199 # # Language mapping 200 # 201 # The `Status` message is the logical representation of the error model, but it 202 # is not necessarily the actual wire format. When the `Status` message is 203 # exposed in different client libraries and different wire protocols, it can be 204 # mapped differently. For example, it will likely be mapped to some exceptions 205 # in Java, but more likely mapped to some error codes in C. 206 # 207 # # Other uses 208 # 209 # The error model and the `Status` message can be used in a variety of 210 # environments, either with or without APIs, to provide a 211 # consistent developer experience across different environments. 212 # 213 # Example uses of this error model include: 214 # 215 # - Partial errors. If a service needs to return partial errors to the client, 216 # it may embed the `Status` in the normal response to indicate the partial 217 # errors. 218 # 219 # - Workflow errors. A typical workflow has multiple steps. Each step may 220 # have a `Status` message for error reporting. 221 # 222 # - Batch operations. If a client uses batch request and batch response, the 223 # `Status` message should be used directly inside batch response, one for 224 # each error sub-response. 225 # 226 # - Asynchronous operations. If an API call embeds asynchronous operation 227 # results in its response, the status of those operations should be 228 # represented directly using the `Status` message. 229 # 230 # - Logging. If some API errors are stored in logs, the message `Status` could 231 # be used directly after any stripping needed for security/privacy reasons. 232 "message": "A String", # A developer-facing error message, which should be in English. Any 233 # user-facing error message should be localized and sent in the 234 # google.rpc.Status.details field, or localized by the client. 235 "code": 42, # The status code, which should be an enum value of google.rpc.Code. 236 "details": [ # A list of messages that carry the error details. There will be a 237 # common set of message types for APIs to use. 238 { 239 "a_key": "", # Properties of the object. Contains field @type with type URL. 240 }, 241 ], 242 }, 243 "done": True or False, # If the value is `false`, it means the operation is still in progress. 244 # If true, the operation is completed, and either `error` or `response` is 245 # available. 246 "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. 247 "a_key": "", # Properties of the object. Contains field @type with type URL. 248 }, 249 "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` 250 }</pre> 251</div> 252 253<div class="method"> 254 <code class="details" id="get">get(readGroupSetId, x__xgafv=None)</code> 255 <pre>Gets a read group set by ID. 256 257For the definitions of read group sets and other genomics resources, see 258[Fundamentals of Google 259Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 260 261Args: 262 readGroupSetId: string, The ID of the read group set. (required) 263 x__xgafv: string, V1 error format. 264 Allowed values 265 1 - v1 error format 266 2 - v2 error format 267 268Returns: 269 An object of the form: 270 271 { # A read group set is a logical collection of read groups, which are 272 # collections of reads produced by a sequencer. A read group set typically 273 # models reads corresponding to one sample, sequenced one way, and aligned one 274 # way. 275 # 276 # * A read group set belongs to one dataset. 277 # * A read group belongs to one read group set. 278 # * A read belongs to one read group. 279 # 280 # For more genomics resource definitions, see [Fundamentals of Google 281 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 282 "info": { # A map of additional read group set information. 283 "a_key": [ 284 "", 285 ], 286 }, 287 "name": "A String", # The read group set name. By default this will be initialized to the sample 288 # name of the sequenced data contained in this set. 289 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read 290 # group set. 291 { # A read group is all the data that's processed the same way by the sequencer. 292 "info": { # A map of additional read group information. This must be of the form 293 # map<string, string[]> (string key mapping to a list of string values). 294 "a_key": [ 295 "", 296 ], 297 }, 298 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length 299 # the sequenced DNA fragment from end-to-end, not including the adapters. 300 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. 301 "programs": [ # The programs used to generate this read group. Programs are always 302 # identical for all read groups within a read group set. For this reason, 303 # only the first read group in a returned set will have this field 304 # populated. 305 { 306 "prevProgramId": "A String", # The ID of the program run before this one. 307 "commandLine": "A String", # The command line used to run this program. 308 "version": "A String", # The version of the program run. 309 "id": "A String", # The user specified locally unique ID of the program. Used along with 310 # `prevProgramId` to define an ordering between programs. 311 "name": "A String", # The display name of the program. This is typically the colloquial name of 312 # the tool used, for example 'bwa' or 'picard'. 313 }, 314 ], 315 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. 316 "experiment": { # The experiment used to generate this read group. 317 "sequencingCenter": "A String", # The sequencing center used as part of this experiment. 318 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA 319 # fragments which have been prepared for sequencing from a sample. This 320 # field is important for quality control as error or bias can be introduced 321 # during sample preparation. 322 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to 323 # sequencing technology in the SAM spec. 324 "platformUnit": "A String", # The platform unit used as part of this experiment, for example 325 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the 326 # @RG PU field in the SAM spec. 327 }, 328 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. 329 "id": "A String", # The server-generated read group ID, unique for all read groups. 330 # Note: This is different than the @RG ID field in the SAM spec. For that 331 # value, see name. 332 "datasetId": "A String", # The dataset to which this read group belongs. 333 "description": "A String", # A free-form text description of this read group. 334 }, 335 ], 336 "filename": "A String", # The filename of the original source file for this read group set, if any. 337 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. 338 "id": "A String", # The server-generated read group set ID, unique for all read group sets. 339 "datasetId": "A String", # The dataset to which this read group set belongs. 340 }</pre> 341</div> 342 343<div class="method"> 344 <code class="details" id="import_">import_(body, x__xgafv=None)</code> 345 <pre>Creates read group sets by asynchronously importing the provided 346information. 347 348For the definitions of read group sets and other genomics resources, see 349[Fundamentals of Google 350Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 351 352The caller must have WRITE permissions to the dataset. 353 354## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import 355 356- Tags will be converted to strings - tag types are not preserved 357- Comments (`@CO`) in the input file header will not be preserved 358- Original header order of references (`@SQ`) will not be preserved 359- Any reverse stranded unmapped reads will be reverse complemented, and 360their qualities (also the "BQ" and "OQ" tags, if any) will be reversed 361- Unmapped reads will be stripped of positional information (reference name 362and position) 363 364Args: 365 body: object, The request body. (required) 366 The object takes the form of: 367 368{ # The read group set import request. 369 "partitionStrategy": "A String", # The partition strategy describes how read groups are partitioned into read 370 # group sets. 371 "sourceUris": [ # A list of URIs pointing at [BAM 372 # files](https://samtools.github.io/hts-specs/SAMv1.pdf) 373 # in Google Cloud Storage. 374 # Those URIs can include wildcards (*), but do not add or remove 375 # matching files before import has completed. 376 # 377 # Note that Google Cloud Storage object listing is only eventually 378 # consistent: files added may be not be immediately visible to 379 # everyone. Thus, if using a wildcard it is preferable not to start 380 # the import immediately after the files are created. 381 "A String", 382 ], 383 "referenceSetId": "A String", # The reference set to which the imported read group sets are aligned to, if 384 # any. The reference names of this reference set must be a superset of those 385 # found in the imported file headers. If no reference set id is provided, a 386 # best effort is made to associate with a matching reference set. 387 "datasetId": "A String", # Required. The ID of the dataset these read group sets will belong to. The 388 # caller must have WRITE permissions to this dataset. 389 } 390 391 x__xgafv: string, V1 error format. 392 Allowed values 393 1 - v1 error format 394 2 - v2 error format 395 396Returns: 397 An object of the form: 398 399 { # This resource represents a long-running operation that is the result of a 400 # network API call. 401 "metadata": { # An OperationMetadata object. This will always be returned with the Operation. 402 "a_key": "", # Properties of the object. Contains field @type with type URL. 403 }, 404 "error": { # The `Status` type defines a logical error model that is suitable for different # The error result of the operation in case of failure or cancellation. 405 # programming environments, including REST APIs and RPC APIs. It is used by 406 # [gRPC](https://github.com/grpc). The error model is designed to be: 407 # 408 # - Simple to use and understand for most users 409 # - Flexible enough to meet unexpected needs 410 # 411 # # Overview 412 # 413 # The `Status` message contains three pieces of data: error code, error message, 414 # and error details. The error code should be an enum value of 415 # google.rpc.Code, but it may accept additional error codes if needed. The 416 # error message should be a developer-facing English message that helps 417 # developers *understand* and *resolve* the error. If a localized user-facing 418 # error message is needed, put the localized message in the error details or 419 # localize it in the client. The optional error details may contain arbitrary 420 # information about the error. There is a predefined set of error detail types 421 # in the package `google.rpc` that can be used for common error conditions. 422 # 423 # # Language mapping 424 # 425 # The `Status` message is the logical representation of the error model, but it 426 # is not necessarily the actual wire format. When the `Status` message is 427 # exposed in different client libraries and different wire protocols, it can be 428 # mapped differently. For example, it will likely be mapped to some exceptions 429 # in Java, but more likely mapped to some error codes in C. 430 # 431 # # Other uses 432 # 433 # The error model and the `Status` message can be used in a variety of 434 # environments, either with or without APIs, to provide a 435 # consistent developer experience across different environments. 436 # 437 # Example uses of this error model include: 438 # 439 # - Partial errors. If a service needs to return partial errors to the client, 440 # it may embed the `Status` in the normal response to indicate the partial 441 # errors. 442 # 443 # - Workflow errors. A typical workflow has multiple steps. Each step may 444 # have a `Status` message for error reporting. 445 # 446 # - Batch operations. If a client uses batch request and batch response, the 447 # `Status` message should be used directly inside batch response, one for 448 # each error sub-response. 449 # 450 # - Asynchronous operations. If an API call embeds asynchronous operation 451 # results in its response, the status of those operations should be 452 # represented directly using the `Status` message. 453 # 454 # - Logging. If some API errors are stored in logs, the message `Status` could 455 # be used directly after any stripping needed for security/privacy reasons. 456 "message": "A String", # A developer-facing error message, which should be in English. Any 457 # user-facing error message should be localized and sent in the 458 # google.rpc.Status.details field, or localized by the client. 459 "code": 42, # The status code, which should be an enum value of google.rpc.Code. 460 "details": [ # A list of messages that carry the error details. There will be a 461 # common set of message types for APIs to use. 462 { 463 "a_key": "", # Properties of the object. Contains field @type with type URL. 464 }, 465 ], 466 }, 467 "done": True or False, # If the value is `false`, it means the operation is still in progress. 468 # If true, the operation is completed, and either `error` or `response` is 469 # available. 470 "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. 471 "a_key": "", # Properties of the object. Contains field @type with type URL. 472 }, 473 "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` 474 }</pre> 475</div> 476 477<div class="method"> 478 <code class="details" id="patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</code> 479 <pre>Updates a read group set. 480 481For the definitions of read group sets and other genomics resources, see 482[Fundamentals of Google 483Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 484 485This method supports patch semantics. 486 487Args: 488 readGroupSetId: string, The ID of the read group set to be updated. The caller must have WRITE 489permissions to the dataset associated with this read group set. (required) 490 body: object, The request body. (required) 491 The object takes the form of: 492 493{ # A read group set is a logical collection of read groups, which are 494 # collections of reads produced by a sequencer. A read group set typically 495 # models reads corresponding to one sample, sequenced one way, and aligned one 496 # way. 497 # 498 # * A read group set belongs to one dataset. 499 # * A read group belongs to one read group set. 500 # * A read belongs to one read group. 501 # 502 # For more genomics resource definitions, see [Fundamentals of Google 503 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 504 "info": { # A map of additional read group set information. 505 "a_key": [ 506 "", 507 ], 508 }, 509 "name": "A String", # The read group set name. By default this will be initialized to the sample 510 # name of the sequenced data contained in this set. 511 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read 512 # group set. 513 { # A read group is all the data that's processed the same way by the sequencer. 514 "info": { # A map of additional read group information. This must be of the form 515 # map<string, string[]> (string key mapping to a list of string values). 516 "a_key": [ 517 "", 518 ], 519 }, 520 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length 521 # the sequenced DNA fragment from end-to-end, not including the adapters. 522 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. 523 "programs": [ # The programs used to generate this read group. Programs are always 524 # identical for all read groups within a read group set. For this reason, 525 # only the first read group in a returned set will have this field 526 # populated. 527 { 528 "prevProgramId": "A String", # The ID of the program run before this one. 529 "commandLine": "A String", # The command line used to run this program. 530 "version": "A String", # The version of the program run. 531 "id": "A String", # The user specified locally unique ID of the program. Used along with 532 # `prevProgramId` to define an ordering between programs. 533 "name": "A String", # The display name of the program. This is typically the colloquial name of 534 # the tool used, for example 'bwa' or 'picard'. 535 }, 536 ], 537 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. 538 "experiment": { # The experiment used to generate this read group. 539 "sequencingCenter": "A String", # The sequencing center used as part of this experiment. 540 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA 541 # fragments which have been prepared for sequencing from a sample. This 542 # field is important for quality control as error or bias can be introduced 543 # during sample preparation. 544 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to 545 # sequencing technology in the SAM spec. 546 "platformUnit": "A String", # The platform unit used as part of this experiment, for example 547 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the 548 # @RG PU field in the SAM spec. 549 }, 550 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. 551 "id": "A String", # The server-generated read group ID, unique for all read groups. 552 # Note: This is different than the @RG ID field in the SAM spec. For that 553 # value, see name. 554 "datasetId": "A String", # The dataset to which this read group belongs. 555 "description": "A String", # A free-form text description of this read group. 556 }, 557 ], 558 "filename": "A String", # The filename of the original source file for this read group set, if any. 559 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. 560 "id": "A String", # The server-generated read group set ID, unique for all read group sets. 561 "datasetId": "A String", # The dataset to which this read group set belongs. 562} 563 564 updateMask: string, An optional mask specifying which fields to update. Supported fields: 565 566* name. 567* referenceSetId. 568 569Leaving `updateMask` unset is equivalent to specifying all mutable 570fields. 571 x__xgafv: string, V1 error format. 572 Allowed values 573 1 - v1 error format 574 2 - v2 error format 575 576Returns: 577 An object of the form: 578 579 { # A read group set is a logical collection of read groups, which are 580 # collections of reads produced by a sequencer. A read group set typically 581 # models reads corresponding to one sample, sequenced one way, and aligned one 582 # way. 583 # 584 # * A read group set belongs to one dataset. 585 # * A read group belongs to one read group set. 586 # * A read belongs to one read group. 587 # 588 # For more genomics resource definitions, see [Fundamentals of Google 589 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 590 "info": { # A map of additional read group set information. 591 "a_key": [ 592 "", 593 ], 594 }, 595 "name": "A String", # The read group set name. By default this will be initialized to the sample 596 # name of the sequenced data contained in this set. 597 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read 598 # group set. 599 { # A read group is all the data that's processed the same way by the sequencer. 600 "info": { # A map of additional read group information. This must be of the form 601 # map<string, string[]> (string key mapping to a list of string values). 602 "a_key": [ 603 "", 604 ], 605 }, 606 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length 607 # the sequenced DNA fragment from end-to-end, not including the adapters. 608 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. 609 "programs": [ # The programs used to generate this read group. Programs are always 610 # identical for all read groups within a read group set. For this reason, 611 # only the first read group in a returned set will have this field 612 # populated. 613 { 614 "prevProgramId": "A String", # The ID of the program run before this one. 615 "commandLine": "A String", # The command line used to run this program. 616 "version": "A String", # The version of the program run. 617 "id": "A String", # The user specified locally unique ID of the program. Used along with 618 # `prevProgramId` to define an ordering between programs. 619 "name": "A String", # The display name of the program. This is typically the colloquial name of 620 # the tool used, for example 'bwa' or 'picard'. 621 }, 622 ], 623 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. 624 "experiment": { # The experiment used to generate this read group. 625 "sequencingCenter": "A String", # The sequencing center used as part of this experiment. 626 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA 627 # fragments which have been prepared for sequencing from a sample. This 628 # field is important for quality control as error or bias can be introduced 629 # during sample preparation. 630 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to 631 # sequencing technology in the SAM spec. 632 "platformUnit": "A String", # The platform unit used as part of this experiment, for example 633 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the 634 # @RG PU field in the SAM spec. 635 }, 636 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. 637 "id": "A String", # The server-generated read group ID, unique for all read groups. 638 # Note: This is different than the @RG ID field in the SAM spec. For that 639 # value, see name. 640 "datasetId": "A String", # The dataset to which this read group belongs. 641 "description": "A String", # A free-form text description of this read group. 642 }, 643 ], 644 "filename": "A String", # The filename of the original source file for this read group set, if any. 645 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. 646 "id": "A String", # The server-generated read group set ID, unique for all read group sets. 647 "datasetId": "A String", # The dataset to which this read group set belongs. 648 }</pre> 649</div> 650 651<div class="method"> 652 <code class="details" id="search">search(body, x__xgafv=None)</code> 653 <pre>Searches for read group sets matching the criteria. 654 655For the definitions of read group sets and other genomics resources, see 656[Fundamentals of Google 657Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 658 659Implements 660[GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). 661 662Args: 663 body: object, The request body. (required) 664 The object takes the form of: 665 666{ # The read group set search request. 667 "pageToken": "A String", # The continuation token, which is used to page through large result sets. 668 # To get the next page of results, set this parameter to the value of 669 # `nextPageToken` from the previous response. 670 "datasetIds": [ # Restricts this query to read group sets within the given datasets. At least 671 # one ID must be provided. 672 "A String", 673 ], 674 "name": "A String", # Only return read group sets for which a substring of the name matches this 675 # string. 676 "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, 677 # defaults to 256. The maximum value is 1024. 678 } 679 680 x__xgafv: string, V1 error format. 681 Allowed values 682 1 - v1 error format 683 2 - v2 error format 684 685Returns: 686 An object of the form: 687 688 { # The read group set search response. 689 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. 690 # Provide this value in a subsequent request to return the next page of 691 # results. This field will be empty if there aren't any additional results. 692 "readGroupSets": [ # The list of matching read group sets. 693 { # A read group set is a logical collection of read groups, which are 694 # collections of reads produced by a sequencer. A read group set typically 695 # models reads corresponding to one sample, sequenced one way, and aligned one 696 # way. 697 # 698 # * A read group set belongs to one dataset. 699 # * A read group belongs to one read group set. 700 # * A read belongs to one read group. 701 # 702 # For more genomics resource definitions, see [Fundamentals of Google 703 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 704 "info": { # A map of additional read group set information. 705 "a_key": [ 706 "", 707 ], 708 }, 709 "name": "A String", # The read group set name. By default this will be initialized to the sample 710 # name of the sequenced data contained in this set. 711 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read 712 # group set. 713 { # A read group is all the data that's processed the same way by the sequencer. 714 "info": { # A map of additional read group information. This must be of the form 715 # map<string, string[]> (string key mapping to a list of string values). 716 "a_key": [ 717 "", 718 ], 719 }, 720 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length 721 # the sequenced DNA fragment from end-to-end, not including the adapters. 722 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. 723 "programs": [ # The programs used to generate this read group. Programs are always 724 # identical for all read groups within a read group set. For this reason, 725 # only the first read group in a returned set will have this field 726 # populated. 727 { 728 "prevProgramId": "A String", # The ID of the program run before this one. 729 "commandLine": "A String", # The command line used to run this program. 730 "version": "A String", # The version of the program run. 731 "id": "A String", # The user specified locally unique ID of the program. Used along with 732 # `prevProgramId` to define an ordering between programs. 733 "name": "A String", # The display name of the program. This is typically the colloquial name of 734 # the tool used, for example 'bwa' or 'picard'. 735 }, 736 ], 737 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. 738 "experiment": { # The experiment used to generate this read group. 739 "sequencingCenter": "A String", # The sequencing center used as part of this experiment. 740 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA 741 # fragments which have been prepared for sequencing from a sample. This 742 # field is important for quality control as error or bias can be introduced 743 # during sample preparation. 744 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to 745 # sequencing technology in the SAM spec. 746 "platformUnit": "A String", # The platform unit used as part of this experiment, for example 747 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the 748 # @RG PU field in the SAM spec. 749 }, 750 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. 751 "id": "A String", # The server-generated read group ID, unique for all read groups. 752 # Note: This is different than the @RG ID field in the SAM spec. For that 753 # value, see name. 754 "datasetId": "A String", # The dataset to which this read group belongs. 755 "description": "A String", # A free-form text description of this read group. 756 }, 757 ], 758 "filename": "A String", # The filename of the original source file for this read group set, if any. 759 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. 760 "id": "A String", # The server-generated read group set ID, unique for all read group sets. 761 "datasetId": "A String", # The dataset to which this read group set belongs. 762 }, 763 ], 764 }</pre> 765</div> 766 767<div class="method"> 768 <code class="details" id="search_next">search_next(previous_request, previous_response)</code> 769 <pre>Retrieves the next page of results. 770 771Args: 772 previous_request: The request for the previous page. (required) 773 previous_response: The response from the request for the previous page. (required) 774 775Returns: 776 A request object that you can call 'execute()' on to request the next 777 page. Returns None if there are no more items in the collection. 778 </pre> 779</div> 780 781</body></html>