{"action":"closed","issue":{"url":"https://api.github.com/repos/psathyrella/partis/issues/49","repository_url":"https://api.github.com/repos/psathyrella/partis","labels_url":"https://api.github.com/repos/psathyrella/partis/issues/49/labels{/name}","comments_url":"https://api.github.com/repos/psathyrella/partis/issues/49/comments","events_url":"https://api.github.com/repos/psathyrella/partis/issues/49/events","html_url":"https://github.com/psathyrella/partis/issues/49","id":53450633,"number":49,"title":"Infer GTR parameters per-person/per-dataset","user":{"login":"psathyrella","id":2960243,"avatar_url":"https://avatars.githubusercontent.com/u/2960243?v=3","gravatar_id":"","url":"https://api.github.com/users/psathyrella","html_url":"https://github.com/psathyrella","followers_url":"https://api.github.com/users/psathyrella/followers","following_url":"https://api.github.com/users/psathyrella/following{/other_user}","gists_url":"https://api.github.com/users/psathyrella/gists{/gist_id}","starred_url":"https://api.github.com/users/psathyrella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/psathyrella/subscriptions","organizations_url":"https://api.github.com/users/psathyrella/orgs","repos_url":"https://api.github.com/users/psathyrella/repos","events_url":"https://api.github.com/users/psathyrella/events{/privacy}","received_events_url":"https://api.github.com/users/psathyrella/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/psathyrella/partis/labels/prio:middling","name":"prio:middling","color":"fbca04"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2015-01-05T21:32:28Z","updated_at":"2016-09-27T19:03:30Z","closed_at":"2016-09-27T19:03:30Z","body":"So right now we infer branch lengths to use in the simulation on the fly for each dataset/person, but we're still using some gtr parameters I got from connor that correspond to one or the other of the people from adaptive. I think this is fine for the moment -- I don't think anything we're doing is sensitive to exactly which base goes to which other base.\r\n\r\nAlthough, note, one thing that we still want to do is account for mutations being more likely from, say, A->C than A->G. This is easy to put in the HMM, but we decided putting it in simulation would be prohibitive so shelved it."}}
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