tra-analysis/website/functions/node_modules/google-proto-files/google/genomics/v1/references.proto
2019-01-06 13:14:45 -06:00

283 lines
11 KiB
Protocol Buffer

// Copyright 2016 Google Inc.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
syntax = "proto3";
package google.genomics.v1;
import "google/api/annotations.proto";
option cc_enable_arenas = true;
option go_package = "google.golang.org/genproto/googleapis/genomics/v1;genomics";
option java_multiple_files = true;
option java_outer_classname = "ReferencesProto";
option java_package = "com.google.genomics.v1";
service ReferenceServiceV1 {
// Searches for reference sets which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
rpc SearchReferenceSets(SearchReferenceSetsRequest) returns (SearchReferenceSetsResponse) {
option (google.api.http) = { post: "/v1/referencesets/search" body: "*" };
}
// Gets a reference set.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
rpc GetReferenceSet(GetReferenceSetRequest) returns (ReferenceSet) {
option (google.api.http) = { get: "/v1/referencesets/{reference_set_id}" };
}
// Searches for references which match the given criteria.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
rpc SearchReferences(SearchReferencesRequest) returns (SearchReferencesResponse) {
option (google.api.http) = { post: "/v1/references/search" body: "*" };
}
// Gets a reference.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
rpc GetReference(GetReferenceRequest) returns (Reference) {
option (google.api.http) = { get: "/v1/references/{reference_id}" };
}
// Lists the bases in a reference, optionally restricted to a range.
//
// For the definitions of references and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
rpc ListBases(ListBasesRequest) returns (ListBasesResponse) {
option (google.api.http) = { get: "/v1/references/{reference_id}/bases" };
}
}
// A reference is a canonical assembled DNA sequence, intended to act as a
// reference coordinate space for other genomic annotations. A single reference
// might represent the human chromosome 1 or mitochandrial DNA, for instance. A
// reference belongs to one or more reference sets.
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
message Reference {
// The server-generated reference ID, unique across all references.
string id = 1;
// The length of this reference's sequence.
int64 length = 2;
// MD5 of the upper-case sequence excluding all whitespace characters (this
// is equivalent to SQ:M5 in SAM). This value is represented in lower case
// hexadecimal format.
string md5checksum = 3;
// The name of this reference, for example `22`.
string name = 4;
// The URI from which the sequence was obtained. Typically specifies a FASTA
// format file.
string source_uri = 5;
// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
// with a version number, for example `GCF_000001405.26`.
repeated string source_accessions = 6;
// ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
int32 ncbi_taxon_id = 7;
}
// A reference set is a set of references which typically comprise a reference
// assembly for a species, such as `GRCh38` which is representative
// of the human genome. A reference set defines a common coordinate space for
// comparing reference-aligned experimental data. A reference set contains 1 or
// more references.
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
message ReferenceSet {
// The server-generated reference set ID, unique across all reference sets.
string id = 1;
// The IDs of the reference objects that are part of this set.
// `Reference.md5checksum` must be unique within this set.
repeated string reference_ids = 2;
// Order-independent MD5 checksum which identifies this reference set. The
// checksum is computed by sorting all lower case hexidecimal string
// `reference.md5checksum` (for all reference in this set) in
// ascending lexicographic order, concatenating, and taking the MD5 of that
// value. The resulting value is represented in lower case hexadecimal format.
string md5checksum = 3;
// ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
// indicating the species which this reference set is intended to model. Note
// that contained references may specify a different `ncbiTaxonId`, as
// assemblies may contain reference sequences which do not belong to the
// modeled species, for example EBV in a human reference genome.
int32 ncbi_taxon_id = 4;
// Free text description of this reference set.
string description = 5;
// Public id of this reference set, such as `GRCh37`.
string assembly_id = 6;
// The URI from which the references were obtained.
string source_uri = 7;
// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
// with a version number, for example `NC_000001.11`.
repeated string source_accessions = 8;
}
message SearchReferenceSetsRequest {
// If present, return reference sets for which the
// [md5checksum][google.genomics.v1.ReferenceSet.md5checksum] matches exactly.
repeated string md5checksums = 1;
// If present, return reference sets for which a prefix of any of
// [sourceAccessions][google.genomics.v1.ReferenceSet.source_accessions]
// match any of these strings. Accession numbers typically have a main number
// and a version, for example `NC_000001.11`.
repeated string accessions = 2;
// If present, return reference sets for which a substring of their
// `assemblyId` matches this string (case insensitive).
string assembly_id = 3;
// 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.
string page_token = 4;
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 4096.
int32 page_size = 5;
}
message SearchReferenceSetsResponse {
// The matching references sets.
repeated ReferenceSet reference_sets = 1;
// 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.
string next_page_token = 2;
}
message GetReferenceSetRequest {
// The ID of the reference set.
string reference_set_id = 1;
}
message SearchReferencesRequest {
// If present, return references for which the
// [md5checksum][google.genomics.v1.Reference.md5checksum] matches exactly.
repeated string md5checksums = 1;
// If present, return references for which a prefix of any of
// [sourceAccessions][google.genomics.v1.Reference.source_accessions] match
// any of these strings. Accession numbers typically have a main number and a
// version, for example `GCF_000001405.26`.
repeated string accessions = 2;
// If present, return only references which belong to this reference set.
string reference_set_id = 3;
// 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.
string page_token = 4;
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 4096.
int32 page_size = 5;
}
message SearchReferencesResponse {
// The matching references.
repeated Reference references = 1;
// 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.
string next_page_token = 2;
}
message GetReferenceRequest {
// The ID of the reference.
string reference_id = 1;
}
message ListBasesRequest {
// The ID of the reference.
string reference_id = 1;
// The start position (0-based) of this query. Defaults to 0.
int64 start = 2;
// The end position (0-based, exclusive) of this query. Defaults to the length
// of this reference.
int64 end = 3;
// 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.
string page_token = 4;
// The maximum number of bases to return in a single page. If unspecified,
// defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
// pairs).
int32 page_size = 5;
}
message ListBasesResponse {
// 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.
int64 offset = 1;
// A substring of the bases that make up this reference.
string sequence = 2;
// 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.
string next_page_token = 3;
}