{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/schemas/issues/655","repository_url":"https://api.github.com/repos/ga4gh/schemas","labels_url":"https://api.github.com/repos/ga4gh/schemas/issues/655/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/schemas/issues/655/comments","events_url":"https://api.github.com/repos/ga4gh/schemas/issues/655/events","html_url":"https://github.com/ga4gh/schemas/pull/655","id":164433362,"number":655,"title":"Calls search endpoint","user":{"login":"david4096","id":3795586,"avatar_url":"https://avatars.githubusercontent.com/u/3795586?v=3","gravatar_id":"","url":"https://api.github.com/users/david4096","html_url":"https://github.com/david4096","followers_url":"https://api.github.com/users/david4096/followers","following_url":"https://api.github.com/users/david4096/following{/other_user}","gists_url":"https://api.github.com/users/david4096/gists{/gist_id}","starred_url":"https://api.github.com/users/david4096/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/david4096/subscriptions","organizations_url":"https://api.github.com/users/david4096/orgs","repos_url":"https://api.github.com/users/david4096/repos","events_url":"https://api.github.com/users/david4096/events{/privacy}","received_events_url":"https://api.github.com/users/david4096/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ga4gh/schemas/labels/in%20progress","name":"in progress","color":"ededed"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-07-07T23:58:55Z","updated_at":"2016-07-12T17:33:19Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/655","html_url":"https://github.com/ga4gh/schemas/pull/655","diff_url":"https://github.com/ga4gh/schemas/pull/655.diff","patch_url":"https://github.com/ga4gh/schemas/pull/655.patch"},"body":"This PR enables variant call data to be queried directly. Currently, call data are only made available in the variant message itself, which makes large sample sets difficult to work with. By enabling a separate endpoint for querying call data we can greatly improve common access patterns without disturbing the existing method.\r\n\r\nThe endpoint, `calls/search` receives a SearchCallsRequest, in which one provides a `variant_set_id`, `call_set_id`, or `variant_id`. This allows pages of Calls to be returned matching the search request as opposed to in a variant message. To carry out these requests and to support the GetCallSet request `variant_id` and `id` have been added to the `Call` message.\r\n\r\nThe existing method of accessing call data is left in place, however, I believe in general this practice of modifying messages at query time to be problematic. It leads to the situation where you have one identifier that could describe two unique returned messages. If this access pattern proves to serve for the same existing use cases we ought to deprecate placing calls in a variant message. For previous discussion on callsets see https://github.com/ga4gh/schemas/issues/583."},"comment":{"url":"https://api.github.com/repos/ga4gh/schemas/issues/comments/232119692","html_url":"https://github.com/ga4gh/schemas/pull/655#issuecomment-232119692","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/655","id":232119692,"user":{"login":"kozbo","id":17557555,"avatar_url":"https://avatars.githubusercontent.com/u/17557555?v=3","gravatar_id":"","url":"https://api.github.com/users/kozbo","html_url":"https://github.com/kozbo","followers_url":"https://api.github.com/users/kozbo/followers","following_url":"https://api.github.com/users/kozbo/following{/other_user}","gists_url":"https://api.github.com/users/kozbo/gists{/gist_id}","starred_url":"https://api.github.com/users/kozbo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kozbo/subscriptions","organizations_url":"https://api.github.com/users/kozbo/orgs","repos_url":"https://api.github.com/users/kozbo/repos","events_url":"https://api.github.com/users/kozbo/events{/privacy}","received_events_url":"https://api.github.com/users/kozbo/received_events","type":"User","site_admin":false},"created_at":"2016-07-12T17:33:19Z","updated_at":"2016-07-12T17:33:19Z","body":"+1  this seems like a great improvement after writing some programs that search the calls using the current scheme. \r\n\r\n@mbaudis @jeromekelleher @jacmarjorie @diekhans Any thoughts?"}}
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