google_api_genomics v0.5.0 GoogleApi.Genomics.V1.Api.Variants View Source

API calls for all endpoints tagged Variants.

Link to this section Summary

Functions

Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.

Merges the given variants with existing variants. Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ], } ] } // New variant with conflicting call information { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } The resulting merged variant would overwrite the existing calls with those from the new variant: { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.

Updates a variant. This method supports patch semantics. Returns the modified variant without its calls.

Link to this section Functions

Link to this function

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

Creates a new variant.

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 (Variant):

Returns

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

Link to this function

genomics_variants_delete(connection, variant_id, optional_params \\ [], opts \\ []) View Source

Deletes a variant.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • variant_id (String.t): The ID of the variant 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

Link to this function

genomics_variants_get(connection, variant_id, optional_params \\ [], opts \\ []) View Source

Gets a variant by ID.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • variant_id (String.t): The ID of the variant.
  • 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.Variant{}} on success {:error, info} on failure

Link to this function

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

Creates variant data by asynchronously importing the provided information. The variants for import will be merged with any existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.

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 (ImportVariantsRequest):

Returns

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

Link to this function

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

Merges the given variants with existing variants. Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ], } ] } // New variant with conflicting call information { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } The resulting merged variant would overwrite the existing calls with those from the new variant: { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.

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 (MergeVariantsRequest):

Returns

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

Link to this function

genomics_variants_patch(connection, variant_id, optional_params \\ [], opts \\ []) View Source

Updates a variant. This method supports patch semantics. Returns the modified variant without its calls.

Parameters

  • connection (GoogleApi.Genomics.V1.Connection): Connection to server
  • variant_id (String.t): The ID of the variant 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. At this time, mutable fields are names and info. Acceptable values are "names" and "info". If unspecified, all mutable fields will be updated.
    • :body (Variant):

Returns

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

Link to this function

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

Gets a list of variants matching the criteria. Implements GlobalAllianceApi.searchVariants.

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 (SearchVariantsRequest):

Returns

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