From 8bbd8d848bc0a5f2c8febc51dcd4b25783dba5c0 Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Thu, 7 Jul 2016 16:25:17 -0700 Subject: [PATCH] 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 | 17 ++++++--------- src/main/proto/ga4gh/reads.proto | 29 ++++++++++++++----------- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/src/main/proto/ga4gh/read_service.proto b/src/main/proto/ga4gh/read_service.proto index 02a7a185..db751059 100644 --- a/src/main/proto/ga4gh/read_service.proto +++ b/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. diff --git a/src/main/proto/ga4gh/reads.proto b/src/main/proto/ga4gh/reads.proto index b5759559..e725842c 100644 --- a/src/main/proto/ga4gh/reads.proto +++ b/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 info = 15; + map 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