google_api_genomics v0.4.0 GoogleApi.Genomics.V1.Api.Readgroupsets View Source
API calls for all endpoints tagged Readgroupsets
.
Link to this section Summary
Functions
Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range. Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.
Deletes a read group set.
Exports a read group set to a BAM file in Google Cloud Storage. 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.
Gets a read group set by ID.
Creates read group sets by asynchronously importing the provided information. The caller must have WRITE permissions to the dataset. ## Notes on BAM 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)
Updates a read group set. This method supports patch semantics.
Searches for read group sets matching the criteria. Implements GlobalAllianceApi.searchReadGroupSets.
Link to this section Functions
genomics_readgroupsets_coveragebuckets_list(connection, read_group_set_id, optional_params \\ [], opts \\ []) View Source
Lists fixed width coverage buckets for a read group set, each of which correspond to a range of a reference sequence. Each bucket summarizes coverage information across its corresponding genomic range. Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.
Parameters
- connection (GoogleApi.Genomics.V1.Connection): Connection to server
- read_group_set_id (String.t): Required. The ID of the read group set over which coverage is requested.
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").
- :end (String.t): The end position of the range on the reference, 0-based exclusive. If specified, `referenceName` must also be specified. If unset or 0, defaults to the length of the reference.
- :pageSize (integer()): The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 2048.
- :pageToken (String.t): 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.
- :referenceName (String.t): The name of the reference to query, within the reference set associated with this query. Optional.
- :start (String.t): The start position of the range on the reference, 0-based inclusive. If specified, `referenceName` must also be specified. Defaults to 0.
- :targetBucketWidth (String.t): The desired width of each reported coverage bucket in base pairs. This will be rounded down to the nearest precomputed bucket width; the value of which is returned as `bucketWidth` in the response. Defaults to infinity (each bucket spans an entire reference sequence) or the length of the target range, if specified. The smallest precomputed `bucketWidth` is currently 2048 base pairs; this is subject to change.
Returns
{:ok, %GoogleApi.Genomics.V1.Model.ListCoverageBucketsResponse{}} on success {:error, info} on failure
genomics_readgroupsets_delete(connection, read_group_set_id, optional_params \\ [], opts \\ []) View Source
Deletes a read group set.
Parameters
- connection (GoogleApi.Genomics.V1.Connection): Connection to server
- read_group_set_id (String.t): 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.
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
genomics_readgroupsets_export(connection, read_group_set_id, optional_params \\ [], opts \\ []) View Source
Exports a read group set to a BAM file in Google Cloud Storage. 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.
Parameters
- connection (GoogleApi.Genomics.V1.Connection): Connection to server
- read_group_set_id (String.t): Required. The ID of the read group set to export. The caller must have READ access to this read group set.
optional_params (KeywordList): [optional] Optional parameters
- :$.xgafv (String.t): V1 error format.
- :access_token (String.t): OAuth access token.
- :alt (String.t): Data format for response.
- :callback (String.t): JSONP
- :fields (String.t): Selector specifying which fields to include in a partial response.
- :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
- :oauth_token (String.t): OAuth 2.0 token for the current user.
- :prettyPrint (boolean()): Returns response with indentations and line breaks.
- :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
- :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
- :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").
- :body (ExportReadGroupSetRequest):
Returns
{:ok, %GoogleApi.Genomics.V1.Model.Operation{}} on success {:error, info} on failure
genomics_readgroupsets_get(connection, read_group_set_id, optional_params \\ [], opts \\ []) View Source
Gets a read group set by ID.
Parameters
- connection (GoogleApi.Genomics.V1.Connection): Connection to server
- read_group_set_id (String.t): The ID of the read group set.
optional_params (KeywordList): [optional] Optional parameters
- :$.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.ReadGroupSet{}} on success {:error, info} on failure
genomics_readgroupsets_import(connection, optional_params \\ [], opts \\ []) View Source
Creates read group sets by asynchronously importing the provided information. The caller must have WRITE permissions to the dataset. ## Notes on BAM 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)
Parameters
- connection (GoogleApi.Genomics.V1.Connection): Connection to server
optional_params (KeywordList): [optional] Optional parameters
- :$.xgafv (String.t): V1 error format.
- :access_token (String.t): OAuth access token.
- :alt (String.t): Data format for response.
- :callback (String.t): JSONP
- :fields (String.t): Selector specifying which fields to include in a partial response.
- :key (String.t): API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.
- :oauth_token (String.t): OAuth 2.0 token for the current user.
- :prettyPrint (boolean()): Returns response with indentations and line breaks.
- :quotaUser (String.t): Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exceed 40 characters.
- :upload_protocol (String.t): Upload protocol for media (e.g. "raw", "multipart").
- :uploadType (String.t): Legacy upload protocol for media (e.g. "media", "multipart").
- :body (ImportReadGroupSetsRequest):
Returns
{:ok, %GoogleApi.Genomics.V1.Model.Operation{}} on success {:error, info} on failure
genomics_readgroupsets_patch(connection, read_group_set_id, optional_params \\ [], opts \\ []) View Source
Updates a read group set. This method supports patch semantics.
Parameters
- connection (GoogleApi.Genomics.V1.Connection): Connection to server
- read_group_set_id (String.t): The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set.
optional_params (KeywordList): [optional] Optional parameters
- :$.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. Supported fields: name. referenceSetId. Leaving `updateMask` unset is equivalent to specifying all mutable fields.
- :body (ReadGroupSet):
Returns
{:ok, %GoogleApi.Genomics.V1.Model.ReadGroupSet{}} on success {:error, info} on failure
genomics_readgroupsets_search(connection, optional_params \\ [], opts \\ []) View Source
Searches for read group sets matching the criteria. Implements GlobalAllianceApi.searchReadGroupSets.
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 (SearchReadGroupSetsRequest):
Returns
{:ok, %GoogleApi.Genomics.V1.Model.SearchReadGroupSetsResponse{}} on success {:error, info} on failure