google_api_genomics v0.4.0 GoogleApi.Genomics.V1.Api.Annotations View Source

API calls for all endpoints tagged Annotations.

Link to this section Summary

Functions

Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together. If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally. For details on the requirements for each individual annotation resource, see CreateAnnotation.

Creates a new annotation. Caller must have WRITE permission for the associated annotation set. The following fields are required: annotationSetId referenceName or referenceId ### Transcripts For annotations of type TRANSCRIPT, the following fields of transcript must be provided: exons.start exons.end All other fields may be optionally specified, unless documented as being server-generated (for example, the `id` field). The annotated range must be no longer than 100Mbp (mega base pairs). See the Annotation resource for additional restrictions on each field.

Deletes an annotation. Caller must have WRITE permission for the associated annotation set.

Gets an annotation. Caller must have READ permission for the associated annotation set.

Searches for annotations that match the given criteria. Results are ordered by genomic coordinate (by reference sequence, then position). Annotations with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotations in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried annotation sets.

Updates an annotation. Caller must have WRITE permission for the associated dataset.

Link to this section Functions

Link to this function

genomics_annotations_batch_create(connection, optional_params \\ [], opts \\ []) View Source

Creates one or more new annotations atomically. All annotations must belong to the same annotation set. Caller must have WRITE permission for this annotation set. For optimal performance, batch positionally adjacent annotations together. If the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will fail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed annotations will be created normally. For details on the requirements for each individual annotation resource, see CreateAnnotation.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • optional_params (KeywordList): [optional] Optional parameters

    • :$.xgafv (String.t): V1 error format.
    • :access_token (String.t): OAuth access token.
    • :alt (String.t): Data format for response.
    • :callback (String.t): JSONP
    • :fields (String.t): Selector specifying which fields to include in a partial response.
    • :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    • :oauth_token (String.t): OAuth 2.0 token for the current user.
    • :prettyPrint (boolean()): Returns response with indentations and line breaks.
    • :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    • :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
    • :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").
    • :body (BatchCreateAnnotationsRequest):

Returns

{:ok, %GoogleApi.Genomics.V1.Model.BatchCreateAnnotationsResponse{}} on success {:error, info} on failure

Link to this function

genomics_annotations_create(connection, optional_params \\ [], opts \\ []) View Source

Creates a new annotation. Caller must have WRITE permission for the associated annotation set. The following fields are required: annotationSetId referenceName or referenceId ### Transcripts For annotations of type TRANSCRIPT, the following fields of transcript must be provided: exons.start exons.end All other fields may be optionally specified, unless documented as being server-generated (for example, the `id` field). The annotated range must be no longer than 100Mbp (mega base pairs). See the Annotation resource for additional restrictions on each field.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • optional_params (KeywordList): [optional] Optional parameters

    • :$.xgafv (String.t): V1 error format.
    • :access_token (String.t): OAuth access token.
    • :alt (String.t): Data format for response.
    • :callback (String.t): JSONP
    • :fields (String.t): Selector specifying which fields to include in a partial response.
    • :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    • :oauth_token (String.t): OAuth 2.0 token for the current user.
    • :prettyPrint (boolean()): Returns response with indentations and line breaks.
    • :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    • :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
    • :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").
    • :body (Annotation):

Returns

{:ok, %GoogleApi.Genomics.V1.Model.Annotation{}} on success {:error, info} on failure

Link to this function

genomics_annotations_delete(connection, annotation_id, optional_params \\ [], opts \\ []) View Source

Deletes an annotation. Caller must have WRITE permission for the associated annotation set.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • annotation_id (String.t): The ID of the annotation to be deleted.
  • optional_params (KeywordList): [optional] Optional parameters

    • :$.xgafv (String.t): V1 error format.
    • :access_token (String.t): OAuth access token.
    • :alt (String.t): Data format for response.
    • :callback (String.t): JSONP
    • :fields (String.t): Selector specifying which fields to include in a partial response.
    • :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    • :oauth_token (String.t): OAuth 2.0 token for the current user.
    • :prettyPrint (boolean()): Returns response with indentations and line breaks.
    • :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    • :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
    • :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").

Returns

{:ok, %GoogleApi.Genomics.V1.Model.Empty{}} on success {:error, info} on failure

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genomics_annotations_get(connection, annotation_id, optional_params \\ [], opts \\ []) View Source

Gets an annotation. Caller must have READ permission for the associated annotation set.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • annotation_id (String.t): The ID of the annotation to be retrieved.
  • optional_params (KeywordList): [optional] Optional parameters

    • :$.xgafv (String.t): V1 error format.
    • :access_token (String.t): OAuth access token.
    • :alt (String.t): Data format for response.
    • :callback (String.t): JSONP
    • :fields (String.t): Selector specifying which fields to include in a partial response.
    • :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    • :oauth_token (String.t): OAuth 2.0 token for the current user.
    • :prettyPrint (boolean()): Returns response with indentations and line breaks.
    • :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    • :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
    • :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").

Returns

{:ok, %GoogleApi.Genomics.V1.Model.Annotation{}} on success {:error, info} on failure

Link to this function

genomics_annotations_search(connection, optional_params \\ [], opts \\ []) View Source

Searches for annotations that match the given criteria. Results are ordered by genomic coordinate (by reference sequence, then position). Annotations with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield annotations in the same order across their respective streams of paginated responses. Caller must have READ permission for the queried annotation sets.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • optional_params (KeywordList): [optional] Optional parameters

    • :$.xgafv (String.t): V1 error format.
    • :access_token (String.t): OAuth access token.
    • :alt (String.t): Data format for response.
    • :callback (String.t): JSONP
    • :fields (String.t): Selector specifying which fields to include in a partial response.
    • :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    • :oauth_token (String.t): OAuth 2.0 token for the current user.
    • :prettyPrint (boolean()): Returns response with indentations and line breaks.
    • :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    • :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
    • :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").
    • :body (SearchAnnotationsRequest):

Returns

{:ok, %GoogleApi.Genomics.V1.Model.SearchAnnotationsResponse{}} on success {:error, info} on failure

Link to this function

genomics_annotations_update(connection, annotation_id, optional_params \\ [], opts \\ []) View Source

Updates an annotation. Caller must have WRITE permission for the associated dataset.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • annotation_id (String.t): The ID of the annotation to be updated.
  • optional_params (KeywordList): [optional] Optional parameters

    • :$.xgafv (String.t): V1 error format.
    • :access_token (String.t): OAuth access token.
    • :alt (String.t): Data format for response.
    • :callback (String.t): JSONP
    • :fields (String.t): Selector specifying which fields to include in a partial response.
    • :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
    • :oauth_token (String.t): OAuth 2.0 token for the current user.
    • :prettyPrint (boolean()): Returns response with indentations and line breaks.
    • :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
    • :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
    • :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").
    • :updateMask (String.t): An optional mask specifying which fields to update. Mutable fields are name, variant, transcript, and info. If unspecified, all mutable fields will be updated.
    • :body (Annotation):

Returns

{:ok, %GoogleApi.Genomics.V1.Model.Annotation{}} on success {:error, info} on failure