{"action":"created","issue":{"url":"https://api.github.com/repos/tnavatar/clingen-data-model/issues/22","labels_url":"https://api.github.com/repos/tnavatar/clingen-data-model/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/tnavatar/clingen-data-model/issues/22/comments","events_url":"https://api.github.com/repos/tnavatar/clingen-data-model/issues/22/events","html_url":"https://github.com/tnavatar/clingen-data-model/issues/22","id":57939204,"number":22,"title":"Revisit coding of start/end","user":{"login":"cbizon","id":10744350,"avatar_url":"https://avatars.githubusercontent.com/u/10744350?v=3","gravatar_id":"","url":"https://api.github.com/users/cbizon","html_url":"https://github.com/cbizon","followers_url":"https://api.github.com/users/cbizon/followers","following_url":"https://api.github.com/users/cbizon/following{/other_user}","gists_url":"https://api.github.com/users/cbizon/gists{/gist_id}","starred_url":"https://api.github.com/users/cbizon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cbizon/subscriptions","organizations_url":"https://api.github.com/users/cbizon/orgs","repos_url":"https://api.github.com/users/cbizon/repos","events_url":"https://api.github.com/users/cbizon/events{/privacy}","received_events_url":"https://api.github.com/users/cbizon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-02-17T15:38:50Z","updated_at":"2015-02-18T14:13:24Z","closed_at":null,"body":"We have decided to use the \"alignment method\", but I would like to have  further discussion about this.  \r\n\r\nThe alignment method works well in a VCF where the point is to keep information about variants.  However, we have separated out variant from coordinate, and now we are using alignment to talk about a coordinate.\r\n\r\nThis is a problem because the coordinate now includes bases that we're not actually interested in.  Two illustrations:\r\n\r\n1) Suppose we have a T in the reference, and in the population there are three alleles: T/A/-.  The deletion of the T must now occur at a different ReferenceCoordinate.\r\n\r\n2) We attach a region type to ReferenceCoordinate independent of any alleles at that location.  Suppose that we have a deletion of the first two bases of an intron.   We would like this to have a regionType of \"splice site\", but our reference coordinate will have to include both the intronic bases, plus one exonic base, meaning that the region type will be something else.\r\n\r\nNote that neither problem is unfixable or unhandleable in the alignment format, but they point, in my mind to a somewhat un-natural way of describing these coordinates: one that sort of requires you to know what the allele is going to be before you define the place where it occurs."},"comment":{"url":"https://api.github.com/repos/tnavatar/clingen-data-model/issues/comments/74869474","html_url":"https://github.com/tnavatar/clingen-data-model/issues/22#issuecomment-74869474","issue_url":"https://api.github.com/repos/tnavatar/clingen-data-model/issues/22","id":74869474,"user":{"login":"sharrison6","id":10516832,"avatar_url":"https://avatars.githubusercontent.com/u/10516832?v=3","gravatar_id":"","url":"https://api.github.com/users/sharrison6","html_url":"https://github.com/sharrison6","followers_url":"https://api.github.com/users/sharrison6/followers","following_url":"https://api.github.com/users/sharrison6/following{/other_user}","gists_url":"https://api.github.com/users/sharrison6/gists{/gist_id}","starred_url":"https://api.github.com/users/sharrison6/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sharrison6/subscriptions","organizations_url":"https://api.github.com/users/sharrison6/orgs","repos_url":"https://api.github.com/users/sharrison6/repos","events_url":"https://api.github.com/users/sharrison6/events{/privacy}","received_events_url":"https://api.github.com/users/sharrison6/received_events","type":"User","site_admin":false},"created_at":"2015-02-18T14:13:24Z","updated_at":"2015-02-18T14:13:24Z","body":"You're right, Chris. rs375794636 was created in build 138. So prior to 138, rs26 and rs375794636 would have been together (I think). However, for the 2 examples I used above, all 4 rs#s were created in 136. So prior to 138 not all rs#s were grouped by position (regardless of type)"}}