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| <h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.readgroupsets.html">readgroupsets</a></h1> | |
| <h2>Instance Methods</h2> | |
| <p class="toc_element"> | |
| <code><a href="genomics_v1.readgroupsets.coveragebuckets.html">coveragebuckets()</a></code> | |
| </p> | |
| <p class="firstline">Returns the coveragebuckets Resource.</p> | |
| <p class="toc_element"> | |
| <code><a href="#delete">delete(readGroupSetId, x__xgafv=None)</a></code></p> | |
| <p class="firstline">Deletes a read group set.</p> | |
| <p class="toc_element"> | |
| <code><a href="#export">export(readGroupSetId, body, x__xgafv=None)</a></code></p> | |
| <p class="firstline">Exports a read group set to a BAM file in Google Cloud Storage.</p> | |
| <p class="toc_element"> | |
| <code><a href="#get">get(readGroupSetId, x__xgafv=None)</a></code></p> | |
| <p class="firstline">Gets a read group set by ID.</p> | |
| <p class="toc_element"> | |
| <code><a href="#import_">import_(body, x__xgafv=None)</a></code></p> | |
| <p class="firstline">Creates read group sets by asynchronously importing the provided</p> | |
| <p class="toc_element"> | |
| <code><a href="#patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</a></code></p> | |
| <p class="firstline">Updates a read group set.</p> | |
| <p class="toc_element"> | |
| <code><a href="#search">search(body, x__xgafv=None)</a></code></p> | |
| <p class="firstline">Searches for read group sets matching the criteria.</p> | |
| <p class="toc_element"> | |
| <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> | |
| <p class="firstline">Retrieves the next page of results.</p> | |
| <h3>Method Details</h3> | |
| <div class="method"> | |
| <code class="details" id="delete">delete(readGroupSetId, x__xgafv=None)</code> | |
| <pre>Deletes a read group set. | |
| For the definitions of read group sets and other genomics resources, see | |
| [Fundamentals of Google | |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| Args: | |
| readGroupSetId: string, The ID of the read group set to be deleted. The caller must have WRITE | |
| permissions to the dataset associated with this read group set. (required) | |
| x__xgafv: string, V1 error format. | |
| Allowed values | |
| 1 - v1 error format | |
| 2 - v2 error format | |
| Returns: | |
| An object of the form: | |
| { # A generic empty message that you can re-use to avoid defining duplicated | |
| # empty messages in your APIs. A typical example is to use it as the request | |
| # or the response type of an API method. For instance: | |
| # | |
| # service Foo { | |
| # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); | |
| # } | |
| # | |
| # The JSON representation for `Empty` is empty JSON object `{}`. | |
| }</pre> | |
| </div> | |
| <div class="method"> | |
| <code class="details" id="export">export(readGroupSetId, body, x__xgafv=None)</code> | |
| <pre>Exports a read group set to a BAM file in Google Cloud Storage. | |
| For the definitions of read group sets and other genomics resources, see | |
| [Fundamentals of Google | |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| Note that currently there may be some differences between exported BAM | |
| files and the original BAM file at the time of import. See | |
| ImportReadGroupSets | |
| for caveats. | |
| Args: | |
| readGroupSetId: string, Required. The ID of the read group set to export. The caller must have | |
| READ access to this read group set. (required) | |
| body: object, The request body. (required) | |
| The object takes the form of: | |
| { # The read group set export request. | |
| "projectId": "A String", # Required. The Google Cloud project ID that owns this | |
| # export. The caller must have WRITE access to this project. | |
| "referenceNames": [ # The reference names to export. If this is not specified, all reference | |
| # sequences, including unmapped reads, are exported. | |
| # Use `*` to export only unmapped reads. | |
| "A String", | |
| ], | |
| "exportUri": "A String", # Required. A Google Cloud Storage URI for the exported BAM file. | |
| # The currently authenticated user must have write access to the new file. | |
| # An error will be returned if the URI already contains data. | |
| } | |
| x__xgafv: string, V1 error format. | |
| Allowed values | |
| 1 - v1 error format | |
| 2 - v2 error format | |
| Returns: | |
| An object of the form: | |
| { # This resource represents a long-running operation that is the result of a | |
| # network API call. | |
| "metadata": { # An OperationMetadata object. This will always be returned with the Operation. | |
| "a_key": "", # Properties of the object. Contains field @type with type URL. | |
| }, | |
| "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. | |
| # programming environments, including REST APIs and RPC APIs. It is used by | |
| # [gRPC](https://github.com/grpc). The error model is designed to be: | |
| # | |
| # - Simple to use and understand for most users | |
| # - Flexible enough to meet unexpected needs | |
| # | |
| # # Overview | |
| # | |
| # The `Status` message contains three pieces of data: error code, error message, | |
| # and error details. The error code should be an enum value of | |
| # google.rpc.Code, but it may accept additional error codes if needed. The | |
| # error message should be a developer-facing English message that helps | |
| # developers *understand* and *resolve* the error. If a localized user-facing | |
| # error message is needed, put the localized message in the error details or | |
| # localize it in the client. The optional error details may contain arbitrary | |
| # information about the error. There is a predefined set of error detail types | |
| # in the package `google.rpc` that can be used for common error conditions. | |
| # | |
| # # Language mapping | |
| # | |
| # The `Status` message is the logical representation of the error model, but it | |
| # is not necessarily the actual wire format. When the `Status` message is | |
| # exposed in different client libraries and different wire protocols, it can be | |
| # mapped differently. For example, it will likely be mapped to some exceptions | |
| # in Java, but more likely mapped to some error codes in C. | |
| # | |
| # # Other uses | |
| # | |
| # The error model and the `Status` message can be used in a variety of | |
| # environments, either with or without APIs, to provide a | |
| # consistent developer experience across different environments. | |
| # | |
| # Example uses of this error model include: | |
| # | |
| # - Partial errors. If a service needs to return partial errors to the client, | |
| # it may embed the `Status` in the normal response to indicate the partial | |
| # errors. | |
| # | |
| # - Workflow errors. A typical workflow has multiple steps. Each step may | |
| # have a `Status` message for error reporting. | |
| # | |
| # - Batch operations. If a client uses batch request and batch response, the | |
| # `Status` message should be used directly inside batch response, one for | |
| # each error sub-response. | |
| # | |
| # - Asynchronous operations. If an API call embeds asynchronous operation | |
| # results in its response, the status of those operations should be | |
| # represented directly using the `Status` message. | |
| # | |
| # - Logging. If some API errors are stored in logs, the message `Status` could | |
| # be used directly after any stripping needed for security/privacy reasons. | |
| "message": "A String", # A developer-facing error message, which should be in English. Any | |
| # user-facing error message should be localized and sent in the | |
| # google.rpc.Status.details field, or localized by the client. | |
| "code": 42, # The status code, which should be an enum value of google.rpc.Code. | |
| "details": [ # A list of messages that carry the error details. There will be a | |
| # common set of message types for APIs to use. | |
| { | |
| "a_key": "", # Properties of the object. Contains field @type with type URL. | |
| }, | |
| ], | |
| }, | |
| "done": True or False, # If the value is `false`, it means the operation is still in progress. | |
| # If true, the operation is completed, and either `error` or `response` is | |
| # available. | |
| "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. | |
| "a_key": "", # Properties of the object. Contains field @type with type URL. | |
| }, | |
| "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` | |
| }</pre> | |
| </div> | |
| <div class="method"> | |
| <code class="details" id="get">get(readGroupSetId, x__xgafv=None)</code> | |
| <pre>Gets a read group set by ID. | |
| For the definitions of read group sets and other genomics resources, see | |
| [Fundamentals of Google | |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| Args: | |
| readGroupSetId: string, The ID of the read group set. (required) | |
| x__xgafv: string, V1 error format. | |
| Allowed values | |
| 1 - v1 error format | |
| 2 - v2 error format | |
| Returns: | |
| An object of the form: | |
| { # A read group set is a logical collection of read groups, which are | |
| # collections of reads produced by a sequencer. A read group set typically | |
| # models reads corresponding to one sample, sequenced one way, and aligned one | |
| # way. | |
| # | |
| # * A read group set belongs to one dataset. | |
| # * A read group belongs to one read group set. | |
| # * A read belongs to one read group. | |
| # | |
| # For more genomics resource definitions, see [Fundamentals of Google | |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| "info": { # A map of additional read group set information. | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "name": "A String", # The read group set name. By default this will be initialized to the sample | |
| # name of the sequenced data contained in this set. | |
| "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read | |
| # group set. | |
| { # A read group is all the data that's processed the same way by the sequencer. | |
| "info": { # A map of additional read group information. This must be of the form | |
| # map<string, string[]> (string key mapping to a list of string values). | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length | |
| # the sequenced DNA fragment from end-to-end, not including the adapters. | |
| "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. | |
| "programs": [ # The programs used to generate this read group. Programs are always | |
| # identical for all read groups within a read group set. For this reason, | |
| # only the first read group in a returned set will have this field | |
| # populated. | |
| { | |
| "prevProgramId": "A String", # The ID of the program run before this one. | |
| "commandLine": "A String", # The command line used to run this program. | |
| "version": "A String", # The version of the program run. | |
| "id": "A String", # The user specified locally unique ID of the program. Used along with | |
| # `prevProgramId` to define an ordering between programs. | |
| "name": "A String", # The display name of the program. This is typically the colloquial name of | |
| # the tool used, for example 'bwa' or 'picard'. | |
| }, | |
| ], | |
| "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. | |
| "experiment": { # The experiment used to generate this read group. | |
| "sequencingCenter": "A String", # The sequencing center used as part of this experiment. | |
| "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA | |
| # fragments which have been prepared for sequencing from a sample. This | |
| # field is important for quality control as error or bias can be introduced | |
| # during sample preparation. | |
| "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to | |
| # sequencing technology in the SAM spec. | |
| "platformUnit": "A String", # The platform unit used as part of this experiment, for example | |
| # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the | |
| # @RG PU field in the SAM spec. | |
| }, | |
| "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. | |
| "id": "A String", # The server-generated read group ID, unique for all read groups. | |
| # Note: This is different than the @RG ID field in the SAM spec. For that | |
| # value, see name. | |
| "datasetId": "A String", # The dataset to which this read group belongs. | |
| "description": "A String", # A free-form text description of this read group. | |
| }, | |
| ], | |
| "filename": "A String", # The filename of the original source file for this read group set, if any. | |
| "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. | |
| "id": "A String", # The server-generated read group set ID, unique for all read group sets. | |
| "datasetId": "A String", # The dataset to which this read group set belongs. | |
| }</pre> | |
| </div> | |
| <div class="method"> | |
| <code class="details" id="import_">import_(body, x__xgafv=None)</code> | |
| <pre>Creates read group sets by asynchronously importing the provided | |
| information. | |
| For the definitions of read group sets and other genomics resources, see | |
| [Fundamentals of Google | |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| The caller must have WRITE permissions to the dataset. | |
| ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import | |
| - Tags will be converted to strings - tag types are not preserved | |
| - Comments (`@CO`) in the input file header will not be preserved | |
| - Original header order of references (`@SQ`) will not be preserved | |
| - Any reverse stranded unmapped reads will be reverse complemented, and | |
| their qualities (also the "BQ" and "OQ" tags, if any) will be reversed | |
| - Unmapped reads will be stripped of positional information (reference name | |
| and position) | |
| Args: | |
| body: object, The request body. (required) | |
| The object takes the form of: | |
| { # The read group set import request. | |
| "partitionStrategy": "A String", # The partition strategy describes how read groups are partitioned into read | |
| # group sets. | |
| "sourceUris": [ # A list of URIs pointing at [BAM | |
| # files](https://samtools.github.io/hts-specs/SAMv1.pdf) | |
| # in Google Cloud Storage. | |
| # Those URIs can include wildcards (*), but do not add or remove | |
| # matching files before import has completed. | |
| # | |
| # Note that Google Cloud Storage object listing is only eventually | |
| # consistent: files added may be not be immediately visible to | |
| # everyone. Thus, if using a wildcard it is preferable not to start | |
| # the import immediately after the files are created. | |
| "A String", | |
| ], | |
| "referenceSetId": "A String", # The reference set to which the imported read group sets are aligned to, if | |
| # any. The reference names of this reference set must be a superset of those | |
| # found in the imported file headers. If no reference set id is provided, a | |
| # best effort is made to associate with a matching reference set. | |
| "datasetId": "A String", # Required. The ID of the dataset these read group sets will belong to. The | |
| # caller must have WRITE permissions to this dataset. | |
| } | |
| x__xgafv: string, V1 error format. | |
| Allowed values | |
| 1 - v1 error format | |
| 2 - v2 error format | |
| Returns: | |
| An object of the form: | |
| { # This resource represents a long-running operation that is the result of a | |
| # network API call. | |
| "metadata": { # An OperationMetadata object. This will always be returned with the Operation. | |
| "a_key": "", # Properties of the object. Contains field @type with type URL. | |
| }, | |
| "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. | |
| # programming environments, including REST APIs and RPC APIs. It is used by | |
| # [gRPC](https://github.com/grpc). The error model is designed to be: | |
| # | |
| # - Simple to use and understand for most users | |
| # - Flexible enough to meet unexpected needs | |
| # | |
| # # Overview | |
| # | |
| # The `Status` message contains three pieces of data: error code, error message, | |
| # and error details. The error code should be an enum value of | |
| # google.rpc.Code, but it may accept additional error codes if needed. The | |
| # error message should be a developer-facing English message that helps | |
| # developers *understand* and *resolve* the error. If a localized user-facing | |
| # error message is needed, put the localized message in the error details or | |
| # localize it in the client. The optional error details may contain arbitrary | |
| # information about the error. There is a predefined set of error detail types | |
| # in the package `google.rpc` that can be used for common error conditions. | |
| # | |
| # # Language mapping | |
| # | |
| # The `Status` message is the logical representation of the error model, but it | |
| # is not necessarily the actual wire format. When the `Status` message is | |
| # exposed in different client libraries and different wire protocols, it can be | |
| # mapped differently. For example, it will likely be mapped to some exceptions | |
| # in Java, but more likely mapped to some error codes in C. | |
| # | |
| # # Other uses | |
| # | |
| # The error model and the `Status` message can be used in a variety of | |
| # environments, either with or without APIs, to provide a | |
| # consistent developer experience across different environments. | |
| # | |
| # Example uses of this error model include: | |
| # | |
| # - Partial errors. If a service needs to return partial errors to the client, | |
| # it may embed the `Status` in the normal response to indicate the partial | |
| # errors. | |
| # | |
| # - Workflow errors. A typical workflow has multiple steps. Each step may | |
| # have a `Status` message for error reporting. | |
| # | |
| # - Batch operations. If a client uses batch request and batch response, the | |
| # `Status` message should be used directly inside batch response, one for | |
| # each error sub-response. | |
| # | |
| # - Asynchronous operations. If an API call embeds asynchronous operation | |
| # results in its response, the status of those operations should be | |
| # represented directly using the `Status` message. | |
| # | |
| # - Logging. If some API errors are stored in logs, the message `Status` could | |
| # be used directly after any stripping needed for security/privacy reasons. | |
| "message": "A String", # A developer-facing error message, which should be in English. Any | |
| # user-facing error message should be localized and sent in the | |
| # google.rpc.Status.details field, or localized by the client. | |
| "code": 42, # The status code, which should be an enum value of google.rpc.Code. | |
| "details": [ # A list of messages that carry the error details. There will be a | |
| # common set of message types for APIs to use. | |
| { | |
| "a_key": "", # Properties of the object. Contains field @type with type URL. | |
| }, | |
| ], | |
| }, | |
| "done": True or False, # If the value is `false`, it means the operation is still in progress. | |
| # If true, the operation is completed, and either `error` or `response` is | |
| # available. | |
| "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. | |
| "a_key": "", # Properties of the object. Contains field @type with type URL. | |
| }, | |
| "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` | |
| }</pre> | |
| </div> | |
| <div class="method"> | |
| <code class="details" id="patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</code> | |
| <pre>Updates a read group set. | |
| For the definitions of read group sets and other genomics resources, see | |
| [Fundamentals of Google | |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| This method supports patch semantics. | |
| Args: | |
| readGroupSetId: string, The ID of the read group set to be updated. The caller must have WRITE | |
| permissions to the dataset associated with this read group set. (required) | |
| body: object, The request body. (required) | |
| The object takes the form of: | |
| { # A read group set is a logical collection of read groups, which are | |
| # collections of reads produced by a sequencer. A read group set typically | |
| # models reads corresponding to one sample, sequenced one way, and aligned one | |
| # way. | |
| # | |
| # * A read group set belongs to one dataset. | |
| # * A read group belongs to one read group set. | |
| # * A read belongs to one read group. | |
| # | |
| # For more genomics resource definitions, see [Fundamentals of Google | |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| "info": { # A map of additional read group set information. | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "name": "A String", # The read group set name. By default this will be initialized to the sample | |
| # name of the sequenced data contained in this set. | |
| "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read | |
| # group set. | |
| { # A read group is all the data that's processed the same way by the sequencer. | |
| "info": { # A map of additional read group information. This must be of the form | |
| # map<string, string[]> (string key mapping to a list of string values). | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length | |
| # the sequenced DNA fragment from end-to-end, not including the adapters. | |
| "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. | |
| "programs": [ # The programs used to generate this read group. Programs are always | |
| # identical for all read groups within a read group set. For this reason, | |
| # only the first read group in a returned set will have this field | |
| # populated. | |
| { | |
| "prevProgramId": "A String", # The ID of the program run before this one. | |
| "commandLine": "A String", # The command line used to run this program. | |
| "version": "A String", # The version of the program run. | |
| "id": "A String", # The user specified locally unique ID of the program. Used along with | |
| # `prevProgramId` to define an ordering between programs. | |
| "name": "A String", # The display name of the program. This is typically the colloquial name of | |
| # the tool used, for example 'bwa' or 'picard'. | |
| }, | |
| ], | |
| "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. | |
| "experiment": { # The experiment used to generate this read group. | |
| "sequencingCenter": "A String", # The sequencing center used as part of this experiment. | |
| "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA | |
| # fragments which have been prepared for sequencing from a sample. This | |
| # field is important for quality control as error or bias can be introduced | |
| # during sample preparation. | |
| "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to | |
| # sequencing technology in the SAM spec. | |
| "platformUnit": "A String", # The platform unit used as part of this experiment, for example | |
| # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the | |
| # @RG PU field in the SAM spec. | |
| }, | |
| "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. | |
| "id": "A String", # The server-generated read group ID, unique for all read groups. | |
| # Note: This is different than the @RG ID field in the SAM spec. For that | |
| # value, see name. | |
| "datasetId": "A String", # The dataset to which this read group belongs. | |
| "description": "A String", # A free-form text description of this read group. | |
| }, | |
| ], | |
| "filename": "A String", # The filename of the original source file for this read group set, if any. | |
| "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. | |
| "id": "A String", # The server-generated read group set ID, unique for all read group sets. | |
| "datasetId": "A String", # The dataset to which this read group set belongs. | |
| } | |
| updateMask: string, An optional mask specifying which fields to update. Supported fields: | |
| * name. | |
| * referenceSetId. | |
| Leaving `updateMask` unset is equivalent to specifying all mutable | |
| fields. | |
| x__xgafv: string, V1 error format. | |
| Allowed values | |
| 1 - v1 error format | |
| 2 - v2 error format | |
| Returns: | |
| An object of the form: | |
| { # A read group set is a logical collection of read groups, which are | |
| # collections of reads produced by a sequencer. A read group set typically | |
| # models reads corresponding to one sample, sequenced one way, and aligned one | |
| # way. | |
| # | |
| # * A read group set belongs to one dataset. | |
| # * A read group belongs to one read group set. | |
| # * A read belongs to one read group. | |
| # | |
| # For more genomics resource definitions, see [Fundamentals of Google | |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| "info": { # A map of additional read group set information. | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "name": "A String", # The read group set name. By default this will be initialized to the sample | |
| # name of the sequenced data contained in this set. | |
| "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read | |
| # group set. | |
| { # A read group is all the data that's processed the same way by the sequencer. | |
| "info": { # A map of additional read group information. This must be of the form | |
| # map<string, string[]> (string key mapping to a list of string values). | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length | |
| # the sequenced DNA fragment from end-to-end, not including the adapters. | |
| "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. | |
| "programs": [ # The programs used to generate this read group. Programs are always | |
| # identical for all read groups within a read group set. For this reason, | |
| # only the first read group in a returned set will have this field | |
| # populated. | |
| { | |
| "prevProgramId": "A String", # The ID of the program run before this one. | |
| "commandLine": "A String", # The command line used to run this program. | |
| "version": "A String", # The version of the program run. | |
| "id": "A String", # The user specified locally unique ID of the program. Used along with | |
| # `prevProgramId` to define an ordering between programs. | |
| "name": "A String", # The display name of the program. This is typically the colloquial name of | |
| # the tool used, for example 'bwa' or 'picard'. | |
| }, | |
| ], | |
| "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. | |
| "experiment": { # The experiment used to generate this read group. | |
| "sequencingCenter": "A String", # The sequencing center used as part of this experiment. | |
| "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA | |
| # fragments which have been prepared for sequencing from a sample. This | |
| # field is important for quality control as error or bias can be introduced | |
| # during sample preparation. | |
| "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to | |
| # sequencing technology in the SAM spec. | |
| "platformUnit": "A String", # The platform unit used as part of this experiment, for example | |
| # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the | |
| # @RG PU field in the SAM spec. | |
| }, | |
| "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. | |
| "id": "A String", # The server-generated read group ID, unique for all read groups. | |
| # Note: This is different than the @RG ID field in the SAM spec. For that | |
| # value, see name. | |
| "datasetId": "A String", # The dataset to which this read group belongs. | |
| "description": "A String", # A free-form text description of this read group. | |
| }, | |
| ], | |
| "filename": "A String", # The filename of the original source file for this read group set, if any. | |
| "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. | |
| "id": "A String", # The server-generated read group set ID, unique for all read group sets. | |
| "datasetId": "A String", # The dataset to which this read group set belongs. | |
| }</pre> | |
| </div> | |
| <div class="method"> | |
| <code class="details" id="search">search(body, x__xgafv=None)</code> | |
| <pre>Searches for read group sets matching the criteria. | |
| For the definitions of read group sets and other genomics resources, see | |
| [Fundamentals of Google | |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| Implements | |
| [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). | |
| Args: | |
| body: object, The request body. (required) | |
| The object takes the form of: | |
| { # The read group set search request. | |
| "pageToken": "A String", # The continuation token, which is used to page through large result sets. | |
| # To get the next page of results, set this parameter to the value of | |
| # `nextPageToken` from the previous response. | |
| "datasetIds": [ # Restricts this query to read group sets within the given datasets. At least | |
| # one ID must be provided. | |
| "A String", | |
| ], | |
| "name": "A String", # Only return read group sets for which a substring of the name matches this | |
| # string. | |
| "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, | |
| # defaults to 256. The maximum value is 1024. | |
| } | |
| x__xgafv: string, V1 error format. | |
| Allowed values | |
| 1 - v1 error format | |
| 2 - v2 error format | |
| Returns: | |
| An object of the form: | |
| { # The read group set search response. | |
| "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. | |
| # Provide this value in a subsequent request to return the next page of | |
| # results. This field will be empty if there aren't any additional results. | |
| "readGroupSets": [ # The list of matching read group sets. | |
| { # A read group set is a logical collection of read groups, which are | |
| # collections of reads produced by a sequencer. A read group set typically | |
| # models reads corresponding to one sample, sequenced one way, and aligned one | |
| # way. | |
| # | |
| # * A read group set belongs to one dataset. | |
| # * A read group belongs to one read group set. | |
| # * A read belongs to one read group. | |
| # | |
| # For more genomics resource definitions, see [Fundamentals of Google | |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) | |
| "info": { # A map of additional read group set information. | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "name": "A String", # The read group set name. By default this will be initialized to the sample | |
| # name of the sequenced data contained in this set. | |
| "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read | |
| # group set. | |
| { # A read group is all the data that's processed the same way by the sequencer. | |
| "info": { # A map of additional read group information. This must be of the form | |
| # map<string, string[]> (string key mapping to a list of string values). | |
| "a_key": [ | |
| "", | |
| ], | |
| }, | |
| "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length | |
| # the sequenced DNA fragment from end-to-end, not including the adapters. | |
| "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. | |
| "programs": [ # The programs used to generate this read group. Programs are always | |
| # identical for all read groups within a read group set. For this reason, | |
| # only the first read group in a returned set will have this field | |
| # populated. | |
| { | |
| "prevProgramId": "A String", # The ID of the program run before this one. | |
| "commandLine": "A String", # The command line used to run this program. | |
| "version": "A String", # The version of the program run. | |
| "id": "A String", # The user specified locally unique ID of the program. Used along with | |
| # `prevProgramId` to define an ordering between programs. | |
| "name": "A String", # The display name of the program. This is typically the colloquial name of | |
| # the tool used, for example 'bwa' or 'picard'. | |
| }, | |
| ], | |
| "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. | |
| "experiment": { # The experiment used to generate this read group. | |
| "sequencingCenter": "A String", # The sequencing center used as part of this experiment. | |
| "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA | |
| # fragments which have been prepared for sequencing from a sample. This | |
| # field is important for quality control as error or bias can be introduced | |
| # during sample preparation. | |
| "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to | |
| # sequencing technology in the SAM spec. | |
| "platformUnit": "A String", # The platform unit used as part of this experiment, for example | |
| # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the | |
| # @RG PU field in the SAM spec. | |
| }, | |
| "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. | |
| "id": "A String", # The server-generated read group ID, unique for all read groups. | |
| # Note: This is different than the @RG ID field in the SAM spec. For that | |
| # value, see name. | |
| "datasetId": "A String", # The dataset to which this read group belongs. | |
| "description": "A String", # A free-form text description of this read group. | |
| }, | |
| ], | |
| "filename": "A String", # The filename of the original source file for this read group set, if any. | |
| "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. | |
| "id": "A String", # The server-generated read group set ID, unique for all read group sets. | |
| "datasetId": "A String", # The dataset to which this read group set belongs. | |
| }, | |
| ], | |
| }</pre> | |
| </div> | |
| <div class="method"> | |
| <code class="details" id="search_next">search_next(previous_request, previous_response)</code> | |
| <pre>Retrieves the next page of results. | |
| Args: | |
| previous_request: The request for the previous page. (required) | |
| previous_response: The response from the request for the previous page. (required) | |
| Returns: | |
| A request object that you can call 'execute()' on to request the next | |
| page. Returns None if there are no more items in the collection. | |
| </pre> | |
| </div> | |
| </body></html> |