{"action":"created","issue":{"url":"https://api.github.com/repos/jts/nanopolish/issues/25","labels_url":"https://api.github.com/repos/jts/nanopolish/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/jts/nanopolish/issues/25/comments","events_url":"https://api.github.com/repos/jts/nanopolish/issues/25/events","html_url":"https://github.com/jts/nanopolish/pull/25","id":114350322,"number":25,"title":"train sd_mean","user":{"login":"mateidavid","id":1039002,"avatar_url":"https://avatars.githubusercontent.com/u/1039002?v=3","gravatar_id":"","url":"https://api.github.com/users/mateidavid","html_url":"https://github.com/mateidavid","followers_url":"https://api.github.com/users/mateidavid/followers","following_url":"https://api.github.com/users/mateidavid/following{/other_user}","gists_url":"https://api.github.com/users/mateidavid/gists{/gist_id}","starred_url":"https://api.github.com/users/mateidavid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mateidavid/subscriptions","organizations_url":"https://api.github.com/users/mateidavid/orgs","repos_url":"https://api.github.com/users/mateidavid/repos","events_url":"https://api.github.com/users/mateidavid/events{/privacy}","received_events_url":"https://api.github.com/users/mateidavid/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-10-30T20:28:56Z","updated_at":"2015-10-30T20:40:54Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/jts/nanopolish/pulls/25","html_url":"https://github.com/jts/nanopolish/pull/25","diff_url":"https://github.com/jts/nanopolish/pull/25.diff","patch_url":"https://github.com/jts/nanopolish/pull/25.patch"},"body":"Initial version of `methyltrain` that trains the model `sd_mean`. This is enabled by the `--stdv` cl option. The code compiles and runs, but I didn't check if the results are actually reasonable.\r\n\r\nApart from training `sd_mean`, I made a few changes to other ares:\r\n\r\n- I moved some of the computation related to `PoreModelStateParams` inside that struct. The problem here is that IGs have 2 parameters but 3 are being used at various points, the problematic overlap being between lambda and sigma. Each time one of them (or eta) is changed, the other has to change, too.\r\n\r\n- Inside `train_one_round`, I moved up (and actually enabled) the code that skips kmers that are not being updated. The loop still writes to the training file and the summary file before continuing. I'm not sure if this is intended, but that's how it worked before, and I din't want to break things."},"comment":{"url":"https://api.github.com/repos/jts/nanopolish/issues/comments/152646283","html_url":"https://github.com/jts/nanopolish/pull/25#issuecomment-152646283","issue_url":"https://api.github.com/repos/jts/nanopolish/issues/25","id":152646283,"user":{"login":"jts","id":389535,"avatar_url":"https://avatars.githubusercontent.com/u/389535?v=3","gravatar_id":"","url":"https://api.github.com/users/jts","html_url":"https://github.com/jts","followers_url":"https://api.github.com/users/jts/followers","following_url":"https://api.github.com/users/jts/following{/other_user}","gists_url":"https://api.github.com/users/jts/gists{/gist_id}","starred_url":"https://api.github.com/users/jts/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jts/subscriptions","organizations_url":"https://api.github.com/users/jts/orgs","repos_url":"https://api.github.com/users/jts/repos","events_url":"https://api.github.com/users/jts/events{/privacy}","received_events_url":"https://api.github.com/users/jts/received_events","type":"User","site_admin":false},"created_at":"2015-10-30T20:40:54Z","updated_at":"2015-10-30T20:40:54Z","body":"Thanks, I did a quick review and the code looks good. Merging."}}