--- /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/genomics/v1/range.proto";
+import "google/genomics/v1/readalignment.proto";
+import "google/genomics/v1/readgroupset.proto";
+import "google/longrunning/operations.proto";
+import "google/protobuf/empty.proto";
+import "google/protobuf/field_mask.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 = "ReadsProto";
+option java_package = "com.google.genomics.v1";
+
+service StreamingReadService {
+ // Returns a stream of all the reads matching the search request, ordered
+ // by reference name, position, and ID.
+ rpc StreamReads(StreamReadsRequest) returns (stream StreamReadsResponse) {
+ option (google.api.http) = {
+ post: "/v1/reads:stream"
+ body: "*"
+ };
+ }
+}
+
+// The Readstore. A data store for DNA sequencing Reads.
+service ReadServiceV1 {
+ // Creates read group sets by asynchronously importing the provided
+ // information.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ //
+ // The caller must have WRITE permissions to the dataset.
+ //
+ // ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) 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)
+ rpc ImportReadGroupSets(ImportReadGroupSetsRequest)
+ returns (google.longrunning.Operation) {
+ option (google.api.http) = {
+ post: "/v1/readgroupsets:import"
+ body: "*"
+ };
+ }
+
+ // Exports a read group set to a BAM file in Google Cloud Storage.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ //
+ // Note that currently there may be some differences between exported BAM
+ // files and the original BAM file at the time of import. See
+ // [ImportReadGroupSets][google.genomics.v1.ReadServiceV1.ImportReadGroupSets]
+ // for caveats.
+ rpc ExportReadGroupSet(ExportReadGroupSetRequest)
+ returns (google.longrunning.Operation) {
+ option (google.api.http) = {
+ post: "/v1/readgroupsets/{read_group_set_id}:export"
+ body: "*"
+ };
+ }
+
+ // Searches for read group sets matching the criteria.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ //
+ // Implements
+ // [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
+ rpc SearchReadGroupSets(SearchReadGroupSetsRequest)
+ returns (SearchReadGroupSetsResponse) {
+ option (google.api.http) = {
+ post: "/v1/readgroupsets/search"
+ body: "*"
+ };
+ }
+
+ // Updates a read group set.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ //
+ // This method supports patch semantics.
+ rpc UpdateReadGroupSet(UpdateReadGroupSetRequest) returns (ReadGroupSet) {
+ option (google.api.http) = {
+ patch: "/v1/readgroupsets/{read_group_set_id}"
+ body: "read_group_set"
+ };
+ }
+
+ // Deletes a read group set.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ rpc DeleteReadGroupSet(DeleteReadGroupSetRequest)
+ returns (google.protobuf.Empty) {
+ option (google.api.http) = {
+ delete: "/v1/readgroupsets/{read_group_set_id}"
+ };
+ }
+
+ // Gets a read group set by ID.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ rpc GetReadGroupSet(GetReadGroupSetRequest) returns (ReadGroupSet) {
+ option (google.api.http) = {
+ get: "/v1/readgroupsets/{read_group_set_id}"
+ };
+ }
+
+ // 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.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ //
+ // 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.
+ rpc ListCoverageBuckets(ListCoverageBucketsRequest)
+ returns (ListCoverageBucketsResponse) {
+ option (google.api.http) = {
+ get: "/v1/readgroupsets/{read_group_set_id}/coveragebuckets"
+ };
+ }
+
+ // Gets a list of reads for one or more read group sets.
+ //
+ // For the definitions of read group sets and other genomics resources, see
+ // [Fundamentals of Google
+ // Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
+ //
+ // Reads search operates over a genomic coordinate space of reference sequence
+ // & position defined over the reference sequences to which the requested
+ // read group sets are aligned.
+ //
+ // If a target positional range is specified, search returns all reads whose
+ // alignment to the reference genome overlap the range. A query which
+ // specifies only read group set IDs yields all reads in those read group
+ // sets, including unmapped reads.
+ //
+ // All reads returned (including reads on subsequent pages) are ordered by
+ // genomic coordinate (by reference sequence, then position). Reads 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 reads in the same order across their respective streams
+ // of paginated responses.
+ //
+ // Implements
+ // [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
+ rpc SearchReads(SearchReadsRequest) returns (SearchReadsResponse) {
+ option (google.api.http) = {
+ post: "/v1/reads/search"
+ body: "*"
+ };
+ }
+}
+
+// The read group set search request.
+message SearchReadGroupSetsRequest {
+ // Restricts this query to read group sets within the given datasets. At least
+ // one ID must be provided.
+ repeated string dataset_ids = 1;
+
+ // Only return read group sets for which a substring of the name matches this
+ // string.
+ string name = 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 = 2;
+
+ // The maximum number of results to return in a single page. If unspecified,
+ // defaults to 256. The maximum value is 1024.
+ int32 page_size = 4;
+}
+
+// The read group set search response.
+message SearchReadGroupSetsResponse {
+ // The list of matching read group sets.
+ repeated ReadGroupSet read_group_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;
+}
+
+// The read group set import request.
+message ImportReadGroupSetsRequest {
+ enum PartitionStrategy {
+ PARTITION_STRATEGY_UNSPECIFIED = 0;
+
+ // In most cases, this strategy yields one read group set per file. This is
+ // the default behavior.
+ //
+ // Allocate one read group set per file per sample. For BAM files, read
+ // groups are considered to share a sample if they have identical sample
+ // names. Furthermore, all reads for each file which do not belong to a read
+ // group, if any, will be grouped into a single read group set per-file.
+ PER_FILE_PER_SAMPLE = 1;
+
+ // Includes all read groups in all imported files into a single read group
+ // set. Requires that the headers for all imported files are equivalent. All
+ // reads which do not belong to a read group, if any, will be grouped into a
+ // separate read group set.
+ MERGE_ALL = 2;
+ }
+
+ // Required. The ID of the dataset these read group sets will belong to. The
+ // caller must have WRITE permissions to this dataset.
+ string dataset_id = 1;
+
+ // The reference set to which the imported read group sets are aligned to, if
+ // any. The reference names of this reference set must be a superset of those
+ // found in the imported file headers. If no reference set id is provided, a
+ // best effort is made to associate with a matching reference set.
+ string reference_set_id = 4;
+
+ // A list of URIs pointing at [BAM
+ // files](https://samtools.github.io/hts-specs/SAMv1.pdf)
+ // in Google Cloud Storage.
+ // Those URIs can include wildcards (*), but do not add or remove
+ // matching files before import has completed.
+ //
+ // Note that Google Cloud Storage object listing is only eventually
+ // consistent: files added may be not be immediately visible to
+ // everyone. Thus, if using a wildcard it is preferable not to start
+ // the import immediately after the files are created.
+ repeated string source_uris = 2;
+
+ // The partition strategy describes how read groups are partitioned into read
+ // group sets.
+ PartitionStrategy partition_strategy = 5;
+}
+
+// The read group set import response.
+message ImportReadGroupSetsResponse {
+ // IDs of the read group sets that were created.
+ repeated string read_group_set_ids = 1;
+}
+
+// The read group set export request.
+message ExportReadGroupSetRequest {
+ // Required. The Google Cloud project ID that owns this
+ // export. The caller must have WRITE access to this project.
+ string project_id = 1;
+
+ // Required. A Google Cloud Storage URI for the exported BAM file.
+ // The currently authenticated user must have write access to the new file.
+ // An error will be returned if the URI already contains data.
+ string export_uri = 2;
+
+ // Required. The ID of the read group set to export. The caller must have
+ // READ access to this read group set.
+ string read_group_set_id = 3;
+
+ // The reference names to export. If this is not specified, all reference
+ // sequences, including unmapped reads, are exported.
+ // Use `*` to export only unmapped reads.
+ repeated string reference_names = 4;
+}
+
+message UpdateReadGroupSetRequest {
+ // 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.
+ string read_group_set_id = 1;
+
+ // The new read group set data. See `updateMask` for details on mutability of
+ // fields.
+ ReadGroupSet read_group_set = 2;
+
+ // An optional mask specifying which fields to update. Supported fields:
+ //
+ // * [name][google.genomics.v1.ReadGroupSet.name].
+ // * [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id].
+ //
+ // Leaving `updateMask` unset is equivalent to specifying all mutable
+ // fields.
+ google.protobuf.FieldMask update_mask = 3;
+}
+
+message DeleteReadGroupSetRequest {
+ // 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.
+ string read_group_set_id = 1;
+}
+
+message GetReadGroupSetRequest {
+ // The ID of the read group set.
+ string read_group_set_id = 1;
+}
+
+message ListCoverageBucketsRequest {
+ // Required. The ID of the read group set over which coverage is requested.
+ string read_group_set_id = 1;
+
+ // The name of the reference to query, within the reference set associated
+ // with this query. Optional.
+ string reference_name = 3;
+
+ // The start position of the range on the reference, 0-based inclusive. If
+ // specified, `referenceName` must also be specified. Defaults to 0.
+ int64 start = 4;
+
+ // 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.
+ int64 end = 5;
+
+ // 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.
+ int64 target_bucket_width = 6;
+
+ // 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 = 7;
+
+ // The maximum number of results to return in a single page. If unspecified,
+ // defaults to 1024. The maximum value is 2048.
+ int32 page_size = 8;
+}
+
+// A bucket over which read coverage has been precomputed. A bucket corresponds
+// to a specific range of the reference sequence.
+message CoverageBucket {
+ // The genomic coordinate range spanned by this bucket.
+ Range range = 1;
+
+ // The average number of reads which are aligned to each individual
+ // reference base in this bucket.
+ float mean_coverage = 2;
+}
+
+message ListCoverageBucketsResponse {
+ // The length of each coverage bucket in base pairs. Note that buckets at the
+ // end of a reference sequence may be shorter. This value is omitted if the
+ // bucket width is infinity (the default behaviour, with no range or
+ // `targetBucketWidth`).
+ int64 bucket_width = 1;
+
+ // The coverage buckets. The list of buckets is sparse; a bucket with 0
+ // overlapping reads is not returned. A bucket never crosses more than one
+ // reference sequence. Each bucket has width `bucketWidth`, unless
+ // its end is the end of the reference sequence.
+ repeated CoverageBucket coverage_buckets = 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;
+}
+
+// The read search request.
+message SearchReadsRequest {
+ // The IDs of the read groups sets within which to search for reads. All
+ // specified read group sets must be aligned against a common set of reference
+ // sequences; this defines the genomic coordinates for the query. Must specify
+ // one of `readGroupSetIds` or `readGroupIds`.
+ repeated string read_group_set_ids = 1;
+
+ // The IDs of the read groups within which to search for reads. All specified
+ // read groups must belong to the same read group sets. Must specify one of
+ // `readGroupSetIds` or `readGroupIds`.
+ repeated string read_group_ids = 5;
+
+ // The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
+ // `*`, only unmapped reads are returned. If unspecified, all reads (mapped
+ // and unmapped) are returned.
+ string reference_name = 7;
+
+ // The start position of the range on the reference, 0-based inclusive. If
+ // specified, `referenceName` must also be specified.
+ int64 start = 8;
+
+ // The end position of the range on the reference, 0-based exclusive. If
+ // specified, `referenceName` must also be specified.
+ int64 end = 9;
+
+ // 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 = 3;
+
+ // The maximum number of results to return in a single page. If unspecified,
+ // defaults to 256. The maximum value is 2048.
+ int32 page_size = 4;
+}
+
+// The read search response.
+message SearchReadsResponse {
+ // The list of matching alignments sorted by mapped genomic coordinate,
+ // if any, ascending in position within the same reference. Unmapped reads,
+ // which have no position, are returned contiguously and are sorted in
+ // ascending lexicographic order by fragment name.
+ repeated Read alignments = 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;
+}
+
+// The stream reads request.
+message StreamReadsRequest {
+ // The Google Cloud project ID which will be billed
+ // for this access. The caller must have WRITE access to this project.
+ // Required.
+ string project_id = 1;
+
+ // The ID of the read group set from which to stream reads.
+ string read_group_set_id = 2;
+
+ // The reference sequence name, for example `chr1`,
+ // `1`, or `chrX`. If set to *, only unmapped reads are
+ // returned.
+ string reference_name = 3;
+
+ // The start position of the range on the reference, 0-based inclusive. If
+ // specified, `referenceName` must also be specified.
+ int64 start = 4;
+
+ // The end position of the range on the reference, 0-based exclusive. If
+ // specified, `referenceName` must also be specified.
+ int64 end = 5;
+
+ // Restricts results to a shard containing approximately `1/totalShards`
+ // of the normal response payload for this query. Results from a sharded
+ // request are disjoint from those returned by all queries which differ only
+ // in their shard parameter. A shard may yield 0 results; this is especially
+ // likely for large values of `totalShards`.
+ //
+ // Valid values are `[0, totalShards)`.
+ int32 shard = 6;
+
+ // Specifying `totalShards` causes a disjoint subset of the normal response
+ // payload to be returned for each query with a unique `shard` parameter
+ // specified. A best effort is made to yield equally sized shards. Sharding
+ // can be used to distribute processing amongst workers, where each worker is
+ // assigned a unique `shard` number and all workers specify the same
+ // `totalShards` number. The union of reads returned for all sharded queries
+ // `[0, totalShards)` is equal to those returned by a single unsharded query.
+ //
+ // Queries for different values of `totalShards` with common divisors will
+ // share shard boundaries. For example, streaming `shard` 2 of 5
+ // `totalShards` yields the same results as streaming `shard`s 4 and 5 of 10
+ // `totalShards`. This property can be leveraged for adaptive retries.
+ int32 total_shards = 7;
+}
+
+message StreamReadsResponse {
+ repeated Read alignments = 1;
+}
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