Revert tag number change

Remove read group set id from search read groups request
Add array of read group ids to read group set

src/main/proto/ga4gh/read_service.proto

@@ -74,12 +74,12 @@ message SearchReadGroupSetsRequest {
 
  // Specifies the maximum number of results to return in a single page.
  // If unspecified, a system default will be used.
- int32 page_size = 3;
+ int32 page_size = 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
  // `next_page_token` from the previous response.
- string page_token = 4;
+ string page_token = 5;
 }
 
 // This is the response from `POST /readgroupsets/search` expressed as JSON.
@@ -105,27 +105,24 @@ message GetReadGroupSetRequest {
 
 
 message SearchReadGroupsRequest {
- // The dataset to search.
+ // The dataset to search (required).
  string dataset_id = 1;
-
- // Only return readgroups within the provided read group set ID.
- string read_group_set_id = 2;
 
  // Only return read groups with this name (case-sensitive, exact match).
- string name = 3;
+ string name = 2;
 
  // Specifying the id of a BioSample record will return only readgroups
  // with the given bioSampleId.
- string bio_sample_id = 4;
+ string bio_sample_id = 3;
 
  // Specifies the maximum number of results to return in a single page.
  // If unspecified, a system default will be used.
- int32 page_size = 5;
+ int32 page_size = 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
  // `next_page_token` from the previous response.
- string page_token = 6;
+ string page_token = 5;
 }
 
 // This is the response from `POST /readgroups/search` expressed as JSON.

src/main/proto/ga4gh/reads.proto

@@ -33,38 +33,38 @@ message ReadGroup {
  string dataset_id = 2;
 
  // The ID of the read group set this read group belongs to.
- string read_group_set_id = 3;
+ string read_group_set_id = 15;
 
  // The read group name.
- string name = 4;
+ string name = 3;
 
  // The read group description.
- string description = 5;
+ string description = 4;
 
  // A name for the sample this read group's data were generated from.
  // This field contains an arbitrary string, typically
  // corresponding to the SM tag in a BAM file.
- string sample_name = 6;
+ string sample_name = 5;
 
  // The BioSample this read group's data was generated from.
- string bio_sample_id = 7;
+ string bio_sample_id = 6;
 
  // The experiment used to generate this read group.
- Experiment experiment = 8;
+ Experiment experiment = 7;
 
  // The predicted insert size of this read group.
- int32 predicted_insert_size = 9;
+ int32 predicted_insert_size = 8;
 
  // The time at which this read group was created in milliseconds from the
  // epoch.
- int64 created = 10;
+ int64 created = 9;
 
  // The time at which this read group was last updated in milliseconds
  // from the epoch.
- int64 updated = 11;
+ int64 updated = 10;
 
  // Statistical data on reads in this read group.
- ReadStats stats = 12;
+ ReadStats stats = 11;
 
  // Program can be used to track the provenance of how read data was generated.
  message Program {
@@ -83,14 +83,14 @@ message ReadGroup {
  // The version of the program run.
  string version = 5;
  }
- repeated Program programs = 13;
+ repeated Program programs = 12;
 
  // The ID of the reference set to which the reads in this read group are
  // aligned. Required if there are any read alignments.
- string reference_set_id = 14;
+ string reference_set_id = 13;
 
  // A map of additional read group information.
- map<string, google.protobuf.ListValue> info = 15;
+ map<string, google.protobuf.ListValue> info = 14;
 }
 
 // A ReadGroupSet is a logical collection of ReadGroups. Typically one
@@ -109,6 +109,9 @@ message ReadGroupSet {
 
  // Statistical data on reads in this read group set.
  ReadStats stats = 4;
+
+ // IDs of the Read Groups in this ReadGroupSet
+ repeated string read_group_ids = 6;
 }
 
 // A linear alignment describes the alignment of a read to a Reference, using a