{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/schemas/issues/352","labels_url":"https://api.github.com/repos/ga4gh/schemas/issues/352/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/schemas/issues/352/comments","events_url":"https://api.github.com/repos/ga4gh/schemas/issues/352/events","html_url":"https://github.com/ga4gh/schemas/pull/352","id":93588475,"number":352,"title":"Move Linear Model to Master Branch","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},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2015-07-07T17:48:41Z","updated_at":"2015-07-21T17:23:49Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/352","html_url":"https://github.com/ga4gh/schemas/pull/352","diff_url":"https://github.com/ga4gh/schemas/pull/352.diff","patch_url":"https://github.com/ga4gh/schemas/pull/352.patch"},"body":"These commits get rid of the entire \"mode\" system, and also all of the graph semantics. Variants in this model are straightforward string replacements that occur at linear coordinate positions.\r\n\r\nThe architecture of Sequences, Segments, and References are all still around, but Joins, Paths, and Alleles are gone.\r\n\r\nSince master has, while this was in development, acquired an Allele annotation branch, some manual integration will be required to adjust what's on master now to the non-existence of the Allele object. Perhaps the Allele annotation stuff would be better housed on the refVar-graph-unary branch, where Alleles are alive and well?"},"comment":{"url":"https://api.github.com/repos/ga4gh/schemas/issues/comments/123408071","html_url":"https://github.com/ga4gh/schemas/pull/352#issuecomment-123408071","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/352","id":123408071,"user":{"login":"calbach","id":822298,"avatar_url":"https://avatars.githubusercontent.com/u/822298?v=3","gravatar_id":"","url":"https://api.github.com/users/calbach","html_url":"https://github.com/calbach","followers_url":"https://api.github.com/users/calbach/followers","following_url":"https://api.github.com/users/calbach/following{/other_user}","gists_url":"https://api.github.com/users/calbach/gists{/gist_id}","starred_url":"https://api.github.com/users/calbach/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/calbach/subscriptions","organizations_url":"https://api.github.com/users/calbach/orgs","repos_url":"https://api.github.com/users/calbach/repos","events_url":"https://api.github.com/users/calbach/events{/privacy}","received_events_url":"https://api.github.com/users/calbach/received_events","type":"User","site_admin":false},"created_at":"2015-07-21T17:23:48Z","updated_at":"2015-07-21T17:23:48Z","body":"Process note: This is massive. Is this an accumulation of changes from many unrelated PRs to the refvar topic branch which have already been individually reviewed? This is problematic as reviewing the actual code in this PR reduces to me having to reread almost the entirety of every avro file in the repo (in many cases without a diff). I will just review the change summary to start.\r\n\r\n> Graphs and graph mode have been removed.\r\n> The Allele object has been removed.\r\n\r\nI'm in favor of this.\r\n\r\n> The sequenceId, start, and length fields on Reference have been replaced with a Segment.\r\n> The referenceId, start, and end fields on SearchVariantsRequest have been replaced with a Segment.\r\n> The referenceName, start, and end fields on Variant have been removed and replaced by a Segment.\r\n\r\nIs there justification for these changes beyond laying the framework for future graph changes? These are pretty significant breaking changes so there should be a tangible benefit.\r\n\r\nAlso, I need to come back to this point and look through the code, but I'm not sure about the reference+sequence relationship. IIRC, a reference ID is also a sequence ID. In the linear branch though, all sequences are references, right? I guess the goal might also be to lay a framework for the future graph changes?\r\n\r\n> IDs have been standardized as the way to refer to Sequences and CallSets.\r\n> The referenceName field of Position has been removed. Positions must now point to Sequences by ID.\r\n> The referenceName field on SearchVariantsRequest has been removed.\r\n> The callSetName field has been removed from Calls; they should now use the callSetId field instead.\r\n\r\nI'd say I'm +0 on this. It's cleaner from a programming perspective, but removal of referenceName and callsetName (i.e. sampleId) functionality will be a barrier to clients when switching from files -> API.\r\n\r\n> Calls now have an id field.\r\n\r\n-1 for performance reasons without hearing some very compelling argument. This is a good example of a case where we should have a separate PR which clearly explains the rationale.\r\n\r\n> The variantId field has been removed from Calls. Calls are to be contained in Variants and cannot be retrieved independently.\r\n\r\nSounds reasonable.\r\n\r\n> The phaseSet of a Call can now only be null or a string, not an array of strings.\r\n\r\nThis seems like another breaking change which needs justification. It may be fine - I just don't have the context.\r\n"}}