--- /dev/null
+// 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";
+import "google/protobuf/empty.proto";
+import "google/protobuf/field_mask.proto";
+import "google/protobuf/struct.proto";
+import "google/protobuf/wrappers.proto";
+import "google/rpc/status.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 = "AnnotationsProto";
+option java_package = "com.google.genomics.v1";
+
+// This service provides storage and positional retrieval of genomic
+// reference annotations, including variant annotations.
+service AnnotationServiceV1 {
+ // Creates a new annotation set. Caller must have WRITE permission for the
+ // associated dataset.
+ //
+ // The following fields are required:
+ //
+ // * [datasetId][google.genomics.v1.AnnotationSet.dataset_id]
+ // * [referenceSetId][google.genomics.v1.AnnotationSet.reference_set_id]
+ //
+ // All other fields may be optionally specified, unless documented as being
+ // server-generated (for example, the `id` field).
+ rpc CreateAnnotationSet(CreateAnnotationSetRequest) returns (AnnotationSet) {
+ option (google.api.http) = {
+ post: "/v1/annotationsets"
+ body: "annotation_set"
+ };
+ }
+
+ // Gets an annotation set. Caller must have READ permission for
+ // the associated dataset.
+ rpc GetAnnotationSet(GetAnnotationSetRequest) returns (AnnotationSet) {
+ option (google.api.http) = {
+ get: "/v1/annotationsets/{annotation_set_id}"
+ };
+ }
+
+ // Updates an annotation set. The update must respect all mutability
+ // restrictions and other invariants described on the annotation set resource.
+ // Caller must have WRITE permission for the associated dataset.
+ rpc UpdateAnnotationSet(UpdateAnnotationSetRequest) returns (AnnotationSet) {
+ option (google.api.http) = {
+ put: "/v1/annotationsets/{annotation_set_id}"
+ body: "annotation_set"
+ };
+ }
+
+ // Deletes an annotation set. Caller must have WRITE permission
+ // for the associated annotation set.
+ rpc DeleteAnnotationSet(DeleteAnnotationSetRequest)
+ returns (google.protobuf.Empty) {
+ option (google.api.http) = {
+ delete: "/v1/annotationsets/{annotation_set_id}"
+ };
+ }
+
+ // Searches for annotation sets that match the given criteria. Annotation sets
+ // are returned in an unspecified order. This order is consistent, such that
+ // two queries for the same content (regardless of page size) yield annotation
+ // sets in the same order across their respective streams of paginated
+ // responses. Caller must have READ permission for the queried datasets.
+ rpc SearchAnnotationSets(SearchAnnotationSetsRequest)
+ returns (SearchAnnotationSetsResponse) {
+ option (google.api.http) = {
+ post: "/v1/annotationsets/search"
+ body: "*"
+ };
+ }
+
+ // Creates a new annotation. Caller must have WRITE permission
+ // for the associated annotation set.
+ //
+ // The following fields are required:
+ //
+ // * [annotationSetId][google.genomics.v1.Annotation.annotation_set_id]
+ // * [referenceName][google.genomics.v1.Annotation.reference_name] or
+ // [referenceId][google.genomics.v1.Annotation.reference_id]
+ //
+ // ### Transcripts
+ //
+ // For annotations of type TRANSCRIPT, the following fields of
+ // [transcript][google.genomics.v1.Annotation.transcript] must be provided:
+ //
+ // * [exons.start][google.genomics.v1.Transcript.Exon.start]
+ // * [exons.end][google.genomics.v1.Transcript.Exon.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][google.genomics.v1.Annotation]
+ // for additional restrictions on each field.
+ rpc CreateAnnotation(CreateAnnotationRequest) returns (Annotation) {
+ option (google.api.http) = {
+ post: "/v1/annotations"
+ body: "annotation"
+ };
+ }
+
+ // 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][google.genomics.v1.AnnotationServiceV1.CreateAnnotation].
+ rpc BatchCreateAnnotations(BatchCreateAnnotationsRequest)
+ returns (BatchCreateAnnotationsResponse) {
+ option (google.api.http) = {
+ post: "/v1/annotations:batchCreate"
+ body: "*"
+ };
+ }
+
+ // Gets an annotation. Caller must have READ permission
+ // for the associated annotation set.
+ rpc GetAnnotation(GetAnnotationRequest) returns (Annotation) {
+ option (google.api.http) = {
+ get: "/v1/annotations/{annotation_id}"
+ };
+ }
+
+ // Updates an annotation. Caller must have
+ // WRITE permission for the associated dataset.
+ rpc UpdateAnnotation(UpdateAnnotationRequest) returns (Annotation) {
+ option (google.api.http) = {
+ put: "/v1/annotations/{annotation_id}"
+ body: "annotation"
+ };
+ }
+
+ // Deletes an annotation. Caller must have WRITE permission for
+ // the associated annotation set.
+ rpc DeleteAnnotation(DeleteAnnotationRequest)
+ returns (google.protobuf.Empty) {
+ option (google.api.http) = {
+ delete: "/v1/annotations/{annotation_id}"
+ };
+ }
+
+ // 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.
+ rpc SearchAnnotations(SearchAnnotationsRequest)
+ returns (SearchAnnotationsResponse) {
+ option (google.api.http) = {
+ post: "/v1/annotations/search"
+ body: "*"
+ };
+ }
+}
+
+// An annotation set is a logical grouping of annotations that share consistent
+// type information and provenance. Examples of annotation sets include 'all
+// genes from refseq', and 'all variant annotations from ClinVar'.
+message AnnotationSet {
+ // The server-generated annotation set ID, unique across all annotation sets.
+ string id = 1;
+
+ // The dataset to which this annotation set belongs.
+ string dataset_id = 2;
+
+ // The ID of the reference set that defines the coordinate space for this
+ // set's annotations.
+ string reference_set_id = 3;
+
+ // The display name for this annotation set.
+ string name = 4;
+
+ // The source URI describing the file from which this annotation set was
+ // generated, if any.
+ string source_uri = 5;
+
+ // The type of annotations contained within this set.
+ AnnotationType type = 6;
+
+ // A map of additional read alignment information. This must be of the form
+ // map<string, string[]> (string key mapping to a list of string values).
+ map<string, google.protobuf.ListValue> info = 17;
+}
+
+// An annotation describes a region of reference genome. The value of an
+// annotation may be one of several canonical types, supplemented by arbitrary
+// info tags. An annotation is not inherently associated with a specific
+// sample or individual (though a client could choose to use annotations in
+// this way). Example canonical annotation types are `GENE` and
+// `VARIANT`.
+message Annotation {
+ // The server-generated annotation ID, unique across all annotations.
+ string id = 1;
+
+ // The annotation set to which this annotation belongs.
+ string annotation_set_id = 2;
+
+ // The display name of this annotation.
+ string name = 3;
+
+ // The ID of the Google Genomics reference associated with this range.
+ string reference_id = 4;
+
+ // The display name corresponding to the reference specified by
+ // `referenceId`, for example `chr1`, `1`, or `chrX`.
+ string reference_name = 5;
+
+ // The start position of the range on the reference, 0-based inclusive.
+ int64 start = 6;
+
+ // The end position of the range on the reference, 0-based exclusive.
+ int64 end = 7;
+
+ // Whether this range refers to the reverse strand, as opposed to the forward
+ // strand. Note that regardless of this field, the start/end position of the
+ // range always refer to the forward strand.
+ bool reverse_strand = 8;
+
+ // The data type for this annotation. Must match the containing annotation
+ // set's type.
+ AnnotationType type = 9;
+
+ oneof value {
+ // A variant annotation, which describes the effect of a variant on the
+ // genome, the coding sequence, and/or higher level consequences at the
+ // organism level e.g. pathogenicity. This field is only set for annotations
+ // of type `VARIANT`.
+ VariantAnnotation variant = 10;
+
+ // A transcript value represents the assertion that a particular region of
+ // the reference genome may be transcribed as RNA. An alternative splicing
+ // pattern would be represented as a separate transcript object. This field
+ // is only set for annotations of type `TRANSCRIPT`.
+ Transcript transcript = 11;
+ }
+
+ // A map of additional read alignment information. This must be of the form
+ // map<string, string[]> (string key mapping to a list of string values).
+ map<string, google.protobuf.ListValue> info = 12;
+}
+
+message VariantAnnotation {
+ message ClinicalCondition {
+ // A set of names for the condition.
+ repeated string names = 1;
+
+ // The set of external IDs for this condition.
+ repeated ExternalId external_ids = 2;
+
+ // The MedGen concept id associated with this gene.
+ // Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ string concept_id = 3;
+
+ // The OMIM id for this condition.
+ // Search for these IDs at http://omim.org/
+ string omim_id = 4;
+ }
+
+ enum Type {
+ TYPE_UNSPECIFIED = 0;
+
+ // `TYPE_OTHER` should be used when no other Type will suffice.
+ // Further explanation of the variant type may be included in the
+ // [info][google.genomics.v1.Annotation.info] field.
+ TYPE_OTHER = 1;
+
+ // `INSERTION` indicates an insertion.
+ INSERTION = 2;
+
+ // `DELETION` indicates a deletion.
+ DELETION = 3;
+
+ // `SUBSTITUTION` indicates a block substitution of
+ // two or more nucleotides.
+ SUBSTITUTION = 4;
+
+ // `SNP` indicates a single nucleotide polymorphism.
+ SNP = 5;
+
+ // `STRUCTURAL` indicates a large structural variant,
+ // including chromosomal fusions, inversions, etc.
+ STRUCTURAL = 6;
+
+ // `CNV` indicates a variation in copy number.
+ CNV = 7;
+ }
+
+ enum Effect {
+ EFFECT_UNSPECIFIED = 0;
+
+ // `EFFECT_OTHER` should be used when no other Effect
+ // will suffice.
+ EFFECT_OTHER = 1;
+
+ // `FRAMESHIFT` indicates a mutation in which the insertion or
+ // deletion of nucleotides resulted in a frameshift change.
+ FRAMESHIFT = 2;
+
+ // `FRAME_PRESERVING_INDEL` indicates a mutation in which a
+ // multiple of three nucleotides has been inserted or deleted, resulting
+ // in no change to the reading frame of the coding sequence.
+ FRAME_PRESERVING_INDEL = 3;
+
+ // `SYNONYMOUS_SNP` indicates a single nucleotide polymorphism
+ // mutation that results in no amino acid change.
+ SYNONYMOUS_SNP = 4;
+
+ // `NONSYNONYMOUS_SNP` indicates a single nucleotide
+ // polymorphism mutation that results in an amino acid change.
+ NONSYNONYMOUS_SNP = 5;
+
+ // `STOP_GAIN` indicates a mutation that leads to the creation
+ // of a stop codon at the variant site. Frameshift mutations creating
+ // downstream stop codons do not count as `STOP_GAIN`.
+ STOP_GAIN = 6;
+
+ // `STOP_LOSS` indicates a mutation that eliminates a
+ // stop codon at the variant site.
+ STOP_LOSS = 7;
+
+ // `SPLICE_SITE_DISRUPTION` indicates that this variant is
+ // found in a splice site for the associated transcript, and alters the
+ // normal splicing pattern.
+ SPLICE_SITE_DISRUPTION = 8;
+ }
+
+ enum ClinicalSignificance {
+ CLINICAL_SIGNIFICANCE_UNSPECIFIED = 0;
+
+ // `OTHER` should be used when no other clinical significance
+ // value will suffice.
+ CLINICAL_SIGNIFICANCE_OTHER = 1;
+
+ UNCERTAIN = 2;
+
+ BENIGN = 3;
+
+ LIKELY_BENIGN = 4;
+
+ LIKELY_PATHOGENIC = 5;
+
+ PATHOGENIC = 6;
+
+ DRUG_RESPONSE = 7;
+
+ HISTOCOMPATIBILITY = 8;
+
+ CONFERS_SENSITIVITY = 9;
+
+ RISK_FACTOR = 10;
+
+ ASSOCIATION = 11;
+
+ PROTECTIVE = 12;
+
+ // `MULTIPLE_REPORTED` should be used when multiple clinical
+ // signficances are reported for a variant. The original clinical
+ // significance values may be provided in the `info` field.
+ MULTIPLE_REPORTED = 13;
+ }
+
+ // Type has been adapted from ClinVar's list of variant types.
+ Type type = 1;
+
+ // Effect of the variant on the coding sequence.
+ Effect effect = 2;
+
+ // The alternate allele for this variant. If multiple alternate alleles
+ // exist at this location, create a separate variant for each one, as they
+ // may represent distinct conditions.
+ string alternate_bases = 3;
+
+ // Google annotation ID of the gene affected by this variant. This should
+ // be provided when the variant is created.
+ string gene_id = 4;
+
+ // Google annotation IDs of the transcripts affected by this variant. These
+ // should be provided when the variant is created.
+ repeated string transcript_ids = 5;
+
+ // The set of conditions associated with this variant.
+ // A condition describes the way a variant influences human health.
+ repeated ClinicalCondition conditions = 6;
+
+ // Describes the clinical significance of a variant.
+ // It is adapted from the ClinVar controlled vocabulary for clinical
+ // significance described at:
+ // http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ ClinicalSignificance clinical_significance = 7;
+}
+
+// A transcript represents the assertion that a particular region of the
+// reference genome may be transcribed as RNA.
+message Transcript {
+ message Exon {
+ // The start position of the exon on this annotation's reference sequence,
+ // 0-based inclusive. Note that this is relative to the reference start, and
+ // **not** the containing annotation start.
+ int64 start = 1;
+
+ // The end position of the exon on this annotation's reference sequence,
+ // 0-based exclusive. Note that this is relative to the reference start, and
+ // *not* the containing annotation start.
+ int64 end = 2;
+
+ // The frame of this exon. Contains a value of 0, 1, or 2, which indicates
+ // the offset of the first coding base of the exon within the reading frame
+ // of the coding DNA sequence, if any. This field is dependent on the
+ // strandedness of this annotation (see
+ // [Annotation.reverse_strand][google.genomics.v1.Annotation.reverse_strand]).
+ // For forward stranded annotations, this offset is relative to the
+ // [exon.start][google.genomics.v1.Transcript.Exon.start]. For reverse
+ // strand annotations, this offset is relative to the
+ // [exon.end][google.genomics.v1.Transcript.Exon.end] `- 1`.
+ //
+ // Unset if this exon does not intersect the coding sequence. Upon creation
+ // of a transcript, the frame must be populated for all or none of the
+ // coding exons.
+ google.protobuf.Int32Value frame = 3;
+ }
+
+ message CodingSequence {
+ // The start of the coding sequence on this annotation's reference sequence,
+ // 0-based inclusive. Note that this position is relative to the reference
+ // start, and *not* the containing annotation start.
+ int64 start = 1;
+
+ // The end of the coding sequence on this annotation's reference sequence,
+ // 0-based exclusive. Note that this position is relative to the reference
+ // start, and *not* the containing annotation start.
+ int64 end = 2;
+ }
+
+ // The annotation ID of the gene from which this transcript is transcribed.
+ string gene_id = 1;
+
+ // The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose
+ // this transcript. This field should be unset for genomes where transcript
+ // splicing does not occur, for example prokaryotes.
+ //
+ // Introns are regions of the transcript that are not included in the
+ // spliced RNA product. Though not explicitly modeled here, intron ranges can
+ // be deduced; all regions of this transcript that are not exons are introns.
+ //
+ // Exonic sequences do not necessarily code for a translational product
+ // (amino acids). Only the regions of exons bounded by the
+ // [codingSequence][google.genomics.v1.Transcript.coding_sequence] correspond
+ // to coding DNA sequence.
+ //
+ // Exons are ordered by start position and may not overlap.
+ repeated Exon exons = 2;
+
+ // The range of the coding sequence for this transcript, if any. To determine
+ // the exact ranges of coding sequence, intersect this range with those of the
+ // [exons][google.genomics.v1.Transcript.exons], if any. If there are any
+ // [exons][google.genomics.v1.Transcript.exons], the
+ // [codingSequence][google.genomics.v1.Transcript.coding_sequence] must start
+ // and end within them.
+ //
+ // Note that in some cases, the reference genome will not exactly match the
+ // observed mRNA transcript e.g. due to variance in the source genome from
+ // reference. In these cases,
+ // [exon.frame][google.genomics.v1.Transcript.Exon.frame] will not necessarily
+ // match the expected reference reading frame and coding exon reference bases
+ // cannot necessarily be concatenated to produce the original transcript mRNA.
+ CodingSequence coding_sequence = 3;
+}
+
+message ExternalId {
+ // The name of the source of this data.
+ string source_name = 1;
+
+ // The id used by the source of this data.
+ string id = 2;
+}
+
+message CreateAnnotationSetRequest {
+ // The annotation set to create.
+ AnnotationSet annotation_set = 1;
+}
+
+message GetAnnotationSetRequest {
+ // The ID of the annotation set to be retrieved.
+ string annotation_set_id = 1;
+}
+
+message UpdateAnnotationSetRequest {
+ // The ID of the annotation set to be updated.
+ string annotation_set_id = 1;
+
+ // The new annotation set.
+ AnnotationSet annotation_set = 2;
+
+ // An optional mask specifying which fields to update. Mutable fields are
+ // [name][google.genomics.v1.AnnotationSet.name],
+ // [source_uri][google.genomics.v1.AnnotationSet.source_uri], and
+ // [info][google.genomics.v1.AnnotationSet.info]. If unspecified, all
+ // mutable fields will be updated.
+ google.protobuf.FieldMask update_mask = 3;
+}
+
+message DeleteAnnotationSetRequest {
+ // The ID of the annotation set to be deleted.
+ string annotation_set_id = 1;
+}
+
+message SearchAnnotationSetsRequest {
+ // Required. The dataset IDs to search within. Caller must have `READ` access
+ // to these datasets.
+ repeated string dataset_ids = 1;
+
+ // If specified, only annotation sets associated with the given reference set
+ // are returned.
+ string reference_set_id = 2;
+
+ // Only return annotations sets for which a substring of the name matches this
+ // string (case insensitive).
+ string name = 3;
+
+ // If specified, only annotation sets that have any of these types are
+ // returned.
+ repeated AnnotationType types = 4;
+
+ // 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 = 5;
+
+ // The maximum number of results to return in a single page. If unspecified,
+ // defaults to 128. The maximum value is 1024.
+ int32 page_size = 6;
+}
+
+message SearchAnnotationSetsResponse {
+ // The matching annotation sets.
+ repeated AnnotationSet annotation_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 CreateAnnotationRequest {
+ // The annotation to be created.
+ Annotation annotation = 1;
+}
+
+message BatchCreateAnnotationsRequest {
+ // The annotations to be created. At most 4096 can be specified in a single
+ // request.
+ repeated Annotation annotations = 1;
+
+ // A unique request ID which enables the server to detect duplicated requests.
+ // If provided, duplicated requests will result in the same response; if not
+ // provided, duplicated requests may result in duplicated data. For a given
+ // annotation set, callers should not reuse `request_id`s when writing
+ // different batches of annotations - behavior in this case is undefined.
+ // A common approach is to use a UUID. For batch jobs where worker crashes are
+ // a possibility, consider using some unique variant of a worker or run ID.
+ string request_id = 2;
+}
+
+message BatchCreateAnnotationsResponse {
+ message Entry {
+ // The creation status.
+ google.rpc.Status status = 1;
+
+ // The created annotation, if creation was successful.
+ Annotation annotation = 2;
+ }
+
+ // The resulting per-annotation entries, ordered consistently with the
+ // original request.
+ repeated Entry entries = 1;
+}
+
+message GetAnnotationRequest {
+ // The ID of the annotation to be retrieved.
+ string annotation_id = 1;
+}
+
+message UpdateAnnotationRequest {
+ // The ID of the annotation to be updated.
+ string annotation_id = 1;
+
+ // The new annotation.
+ Annotation annotation = 2;
+
+ // An optional mask specifying which fields to update. Mutable fields are
+ // [name][google.genomics.v1.Annotation.name],
+ // [variant][google.genomics.v1.Annotation.variant],
+ // [transcript][google.genomics.v1.Annotation.transcript], and
+ // [info][google.genomics.v1.Annotation.info]. If unspecified, all mutable
+ // fields will be updated.
+ google.protobuf.FieldMask update_mask = 3;
+}
+
+message DeleteAnnotationRequest {
+ // The ID of the annotation to be deleted.
+ string annotation_id = 1;
+}
+
+message SearchAnnotationsRequest {
+ // Required. The annotation sets to search within. The caller must have
+ // `READ` access to these annotation sets.
+ // All queried annotation sets must have the same type.
+ repeated string annotation_set_ids = 1;
+
+ // Required. `reference_id` or `reference_name` must be set.
+ oneof reference {
+ // The ID of the reference to query.
+ string reference_id = 2;
+
+ // The name of the reference to query, within the reference set associated
+ // with this query.
+ string reference_name = 3;
+ }
+
+ // The start position of the range on the reference, 0-based inclusive. If
+ // specified,
+ // [referenceId][google.genomics.v1.SearchAnnotationsRequest.reference_id] or
+ // [referenceName][google.genomics.v1.SearchAnnotationsRequest.reference_name]
+ // must be specified. Defaults to 0.
+ int64 start = 4;
+
+ // The end position of the range on the reference, 0-based exclusive. If
+ // [referenceId][google.genomics.v1.SearchAnnotationsRequest.reference_id] or
+ // [referenceName][google.genomics.v1.SearchAnnotationsRequest.reference_name]
+ // must be specified, Defaults to the length of the reference.
+ int64 end = 5;
+
+ // 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 = 6;
+
+ // The maximum number of results to return in a single page. If unspecified,
+ // defaults to 256. The maximum value is 2048.
+ int32 page_size = 7;
+}
+
+message SearchAnnotationsResponse {
+ // The matching annotations.
+ repeated Annotation annotations = 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;
+}
+
+// When an [Annotation][google.genomics.v1.Annotation] or
+// [AnnotationSet][google.genomics.v1.AnnotationSet] is created, if `type` is
+// not specified it will be set to `GENERIC`.
+enum AnnotationType {
+ ANNOTATION_TYPE_UNSPECIFIED = 0;
+
+ // A `GENERIC` annotation type should be used when no other annotation
+ // type will suffice. This represents an untyped annotation of the reference
+ // genome.
+ GENERIC = 1;
+
+ // A `VARIANT` annotation type.
+ VARIANT = 2;
+
+ // A `GENE` annotation type represents the existence of a gene at the
+ // associated reference coordinates. The start coordinate is typically the
+ // gene's transcription start site and the end is typically the end of the
+ // gene's last exon.
+ GENE = 3;
+
+ // A `TRANSCRIPT` annotation type represents the assertion that a
+ // particular region of the reference genome may be transcribed as RNA.
+ TRANSCRIPT = 4;
+}
git://repos.xcallymotion.com / motion2.git / blobdiff