// Copyright 2024 Google LLC
//
// 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/readgroup.proto";
import "google/protobuf/struct.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 = "ReadGroupSetProto";
option java_package = "com.google.genomics.v1";

// A read group set is a logical collection of read groups, which are
// collections of reads produced by a sequencer. A read group set typically
// models reads corresponding to one sample, sequenced one way, and aligned one
// way.
//
// * A read group set belongs to one dataset.
// * A read group belongs to one read group set.
// * A read belongs to one read group.
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
message ReadGroupSet {
  // The server-generated read group set ID, unique for all read group sets.
  string id = 1;

  // The dataset to which this read group set belongs.
  string dataset_id = 2;

  // The reference set to which the reads in this read group set are aligned.
  string reference_set_id = 3;

  // The read group set name. By default this will be initialized to the sample
  // name of the sequenced data contained in this set.
  string name = 4;

  // The filename of the original source file for this read group set, if any.
  string filename = 5;

  // The read groups in this set. There are typically 1-10 read groups in a read
  // group set.
  repeated ReadGroup read_groups = 6;

  // A map of additional read group set information.
  map<string, google.protobuf.ListValue> info = 7;
}