{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/schemas/issues/162","labels_url":"https://api.github.com/repos/ga4gh/schemas/issues/162/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/schemas/issues/162/comments","events_url":"https://api.github.com/repos/ga4gh/schemas/issues/162/events","html_url":"https://github.com/ga4gh/schemas/pull/162","id":45695729,"number":162,"title":"Adding sequence records, and cleaning up reference records.","user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ga4gh/schemas/labels/ReadTaskTeam","name":"ReadTaskTeam","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":14,"created_at":"2014-10-13T23:08:34Z","updated_at":"2015-02-24T23:23:38Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/162","html_url":"https://github.com/ga4gh/schemas/pull/162","diff_url":"https://github.com/ga4gh/schemas/pull/162.diff","patch_url":"https://github.com/ga4gh/schemas/pull/162.patch"},"body":"@jeromekelleher and I plotted this one out this PM; we think this is a more consistent and general approach to serving references and sequences. Specifically, we:\r\n\r\n* Added `GASequence` and `GASequenceFragment` models. These models define a _generic_ contig sequence, which could be used to describe a reference assembly, a _de novo_ assembly, variant calls spliced back into a reference assembly, etc...\r\n* Cleaned up a few fields in `GAReference` and `GAReferenceSet` to make the relations of the models slightly cleaner/clearer.\r\n* Removed `/references/{id}/bases` GET request. Instead, we have added `/sequences/{id}` and /sequencefragments/{id}` GET requests, which are more general."},"comment":{"url":"https://api.github.com/repos/ga4gh/schemas/issues/comments/75870935","html_url":"https://github.com/ga4gh/schemas/pull/162#issuecomment-75870935","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/162","id":75870935,"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},"created_at":"2015-02-24T23:23:38Z","updated_at":"2015-02-24T23:23:38Z","body":"I think we should think about what we want to do with this in light of #238. Right now in the API we have a concept of a \"sequence\", which is a string with an associated ID and end joins onto other sequences, and we have a way to page through the bases of a sequence. We also still have the `/references/{id}/bases` call lying around.\r\n\r\nThe simplest thing would be to close this up and run with the sequence system we have, but I still think what we have is kinda ugly, and so would be open to changing it around.\r\n\r\n"}}