{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/88","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/88/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/88/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/88/events","html_url":"https://github.com/cjfields/redmine-test/issues/88","id":108470620,"number":88,"title":"Codeml (v 4v4d) using fixed kappa value, reports wrong kappa","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Priority:%20Normal","name":"Priority: Normal","color":"666600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"FF6600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Tracker:%20Bug","name":"Tracker: Bug","color":"FF0000"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-09-26T14:29:01Z","updated_at":"2015-09-26T14:29:03Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Janet Young** (Janet Young)\nOriginal Redmine Issue: 3331, https://redmine.open-bio.org/issues/3331\nOriginal Date: 2012-03-06\nOriginal Assignee: Bioperl Guts\n\n---\n\nHi there,\n\nAfter a long absence, I’ve started using Bioperl to run PAML again. Apologies if I’m bringing up another one of those annoying “PAML changed and broke the parser” kinds of issues… Is PAML v4.4d supported?\n\nI found a minor bug/issue I thought you might want to know about: if I set up a ka\\_ks\\_factory and specify fix\\_kappa = 1, then I recover the kappa via get\\_MLmatrix, it actually reports to me the omega (not the kappa). I’ll attach a script that shows this (I’ll include output as comments in the script). I think the example script should explain everything, but please let me know if you need more details…\n\nthanks very much,\n\nJanet Young\n\n------------------------------------------------------------------------\n\nDr. Janet Young\n\nTapscott and Malik labs\n\nFred Hutchinson Cancer Research Center\n1100 Fairview Avenue N., C3-168,\nP.O. Box 19024, Seattle, WA 98109-1024, USA.\n\nemail: jayoung …at… fhcrc.org\n\n------------------------------------------------------------------------\n\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/143454801","html_url":"https://github.com/cjfields/redmine-test/issues/88#issuecomment-143454801","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/88","id":143454801,"user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"created_at":"2015-09-26T14:29:03Z","updated_at":"2015-09-26T14:29:03Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Jason Stajich** (Jason Stajich)\nOriginal Date: 2012-03-13T16:53:53Z\n\n---\n\nYou are definitely the first to use/report on 4.4d… hopefully someone can look at it quickly as it sounds like a quick fix.\n\n"}}