reference_service

ListReferenceBases(request)

Parameters:request – ListReferenceBasesRequest Return type:ListReferenceBasesResponse Throws:GAException

Lists Reference bases by ID and optional range.

POST /listreferencebases will return a JSON version of ListReferenceBasesResponse.

GetReferenceSet(request)

Parameters:request – GetReferenceSetRequest Return type:ReferenceSet Throws:GAException

Gets a ReferenceSet by ID.

GET /referencesets/{reference_set_id} will return a JSON version of ReferenceSet.

SearchReferenceSets(request)

Parameters:request – SearchReferenceSetsRequest Return type:SearchReferenceSetsResponse Throws:GAException

Gets a list of ReferenceSet matching the search criteria.

POST /referencesets/search must accept a JSON version of SearchReferenceSetsRequest as the post body and will return a JSON version of SearchReferenceSetsResponse.

SearchReferences(request)

Parameters:request – SearchReferencesRequest Return type:SearchReferencesResponse Throws:GAException

Gets a list of Reference matching the search criteria.

POST /references/search must accept a JSON version of SearchReferencesRequest as the post body and will return a JSON version of SearchReferencesResponse.

GetReference(request)

Parameters:request – GetReferenceRequest Return type:Reference Throws:GAException

Gets a Reference by ID.

GET /references/{reference_id} will return a JSON version of Reference.

message SearchReferenceSetsRequest

Fields:

• md5checksum (string) – If unset, return the reference sets for which the md5checksum matches this string (case-sensitive, exact match). See ReferenceSet::md5checksum for details.
• accession (string) – If unset, return the reference sets for which the accession matches this string (case-sensitive, exact match).
• assembly_id (string) – If unset, return the reference sets for which the assemblyId matches this string (case-sensitive, exact match).
• page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
• page_token (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 next_page_token from the previous response.

************ /referencesets *************** This request maps to the body of POST /referencesets/search as JSON.

message SearchReferenceSetsResponse

Fields:

• reference_sets (list of ReferenceSet) – The list of matching reference sets.
• next_page_token (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.

This is the response from POST /referencesets/search expressed as JSON.

message GetReferenceSetRequest

Fields:

• reference_set_id (string) – The ID of the ReferenceSet to be retrieved.

This request maps to the URL GET /referencesets/{reference_set_id}.

message SearchReferencesRequest

Fields:

• reference_set_id (string) – The ReferenceSet to search.
• md5checksum (string) – If specified, return the references for which the md5checksum matches this string (case-sensitive, exact match). See ReferenceSet::md5checksum for details.
• accession (string) – If specified, return the references for which the accession matches this string (case-sensitive, exact match).
• page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
• page_token (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 next_page_token from the previous response.

************ /references *************** This request maps to the body of POST /references/search as JSON.

message SearchReferencesResponse

Fields:

• references (list of Reference) – The list of matching references.
• next_page_token (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.

This is the response from POST /references/search expressed as JSON.

message GetReferenceRequest

Fields:

• reference_id (string) – The ID of the Reference to be retrieved.

This request maps to the URL GET /references/{reference_id}.

message ListReferenceBasesRequest

Fields:

• reference_id (string) – The ID of the Reference to be retrieved.
• start (long) – The start position (0-based) of this query. Defaults to 0. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).
• end (long) – The end position (0-based, exclusive) of this query. Defaults to the length of this Reference.
• page_token (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 next_page_token from the previous response.

This request retrieves a region of a reference genome when sent to the /listreferencebases endpoint.

message ListReferenceBasesResponse

Fields:

• offset (long) – The offset position (0-based) of the given sequence from the start of this Reference. This value will differ for each page in a paginated request.
• sequence (string) – A substring of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regexp [ACGTMRWSYKVHDBN]*.
• next_page_token (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.

The response from POST /listreferencebases expressed as JSON.