{"action":"created","comment":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/26672195","id":26672195,"diff_hunk":"@@ -261,17 +260,89 @@ ListReferenceBasesResponse getReferenceBases(\n   /** Additional request parameters to restrict the query. */\n   ListReferenceBasesRequest request) throws GAException;\n \n-/****************  /sequence/{id}  *******************/\n+/******************  /sequences/search  *********************/\n+/**\n+This request maps to the body of `POST /sequences/search` as JSON.\n+*/\n+record SearchSequencesRequest {\n+  /**\n+  If not null, return only `Sequence`s that appear in the indicated\n+  `ReferenceSet`, or any included `ReferenceSet`s.","path":"src/main/resources/avro/referencemethods.avdl","position":37,"original_position":37,"commit_id":"7df14fb10f10a383713894d5f9d6cdee28776cec","original_commit_id":"7df14fb10f10a383713894d5f9d6cdee28776cec","user":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"body":"I don't understand the last clause: \"... or any included `ReferenceSet`s.\". What do you mean here?","created_at":"2015-03-18T15:16:08Z","updated_at":"2015-03-18T15:16:08Z","html_url":"https://github.com/ga4gh/schemas/pull/250#discussion_r26672195","pull_request_url":"https://api.github.com/repos/ga4gh/schemas/pulls/250","_links":{"self":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/26672195"},"html":{"href":"https://github.com/ga4gh/schemas/pull/250#discussion_r26672195"},"pull_request":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/250"}}},"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/250","id":30685801,"html_url":"https://github.com/ga4gh/schemas/pull/250","diff_url":"https://github.com/ga4gh/schemas/pull/250.diff","patch_url":"https://github.com/ga4gh/schemas/pull/250.patch","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/250","number":250,"state":"open","locked":false,"title":"Side graphs: `Sequence`s and `Join`s","user":{"login":"adamnovak","id":5062495,"avatar_url":"https://avatars.githubusercontent.com/u/5062495?v=3","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"body":"Here's a draft of what our graph model would look like if instead of the \"insert graphs\" we are using now (where sequences come with associated end joins), we used a \"side graph\". In a side graph, we split out `Sequence`s (which are just strings with IDs) and `Join`s (which bind two sides of two bases in two sequences together). Both kinds of objects, in this world, can occur in `ReferenceSet`s and `VariantSet`s.\r\n\r\nI've made a bunch of API changes to see how that would actually work: creating a `Sequence` object, to start with. @richarddurbin made `Join`s, and then I changed the methods for searching to give us nice clean `searchSequences()` and `searchJoins()` methods to get them.\r\n\r\n@richarddurbin: is this what you were going for?\r\n\r\n@lh3: have I captured side graphs correctly?\r\n\r\nAll: do we actually like side graphs better than insert graphs?\r\n\r\nI don't expect this to be merged for a while, but I think we need a concrete proposal to help anchor the discussion in #243 and its ensuing massive e-mail 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