{"action":"created","issue":{"url":"https://api.github.com/repos/yuchaojiang/CODEX2/issues/3","repository_url":"https://api.github.com/repos/yuchaojiang/CODEX2","labels_url":"https://api.github.com/repos/yuchaojiang/CODEX2/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/yuchaojiang/CODEX2/issues/3/comments","events_url":"https://api.github.com/repos/yuchaojiang/CODEX2/issues/3/events","html_url":"https://github.com/yuchaojiang/CODEX2/issues/3","id":323924519,"number":3,"title":"codex2_targeted.R, getcoverage error","user":{"login":"thedam","id":634773,"avatar_url":"https://avatars1.githubusercontent.com/u/634773?v=4","gravatar_id":"","url":"https://api.github.com/users/thedam","html_url":"https://github.com/thedam","followers_url":"https://api.github.com/users/thedam/followers","following_url":"https://api.github.com/users/thedam/following{/other_user}","gists_url":"https://api.github.com/users/thedam/gists{/gist_id}","starred_url":"https://api.github.com/users/thedam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thedam/subscriptions","organizations_url":"https://api.github.com/users/thedam/orgs","repos_url":"https://api.github.com/users/thedam/repos","events_url":"https://api.github.com/users/thedam/events{/privacy}","received_events_url":"https://api.github.com/users/thedam/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-17T08:39:17Z","updated_at":"2018-05-17T11:38:58Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\nThis function return an error:\r\nhttps://github.com/yuchaojiang/CODEX2/blob/dcd1be53342c10b9100fb3eb6603228e256471ab/targeted_sequencing/codex2_targeted.R#L22\r\n\r\n>  \\> coverageObj=getcoverage(bambedObj,mapqthres=20)\r\n> Error in message(\"Getting coverage for chr \", chr, sep = \"\") : \r\n>   argument \"chr\" is missing, with no default\r\n\r\n\r\n```\r\n?getcoverage\r\ngetcoverage {CODEX2}\r\n(...)\r\ngetcoverage(bambedObj, mapqthres, chr)\r\n```\r\nCheers\r\nDamian Loska"},"comment":{"url":"https://api.github.com/repos/yuchaojiang/CODEX2/issues/comments/389837039","html_url":"https://github.com/yuchaojiang/CODEX2/issues/3#issuecomment-389837039","issue_url":"https://api.github.com/repos/yuchaojiang/CODEX2/issues/3","id":389837039,"user":{"login":"yuchaojiang","id":10134217,"avatar_url":"https://avatars2.githubusercontent.com/u/10134217?v=4","gravatar_id":"","url":"https://api.github.com/users/yuchaojiang","html_url":"https://github.com/yuchaojiang","followers_url":"https://api.github.com/users/yuchaojiang/followers","following_url":"https://api.github.com/users/yuchaojiang/following{/other_user}","gists_url":"https://api.github.com/users/yuchaojiang/gists{/gist_id}","starred_url":"https://api.github.com/users/yuchaojiang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yuchaojiang/subscriptions","organizations_url":"https://api.github.com/users/yuchaojiang/orgs","repos_url":"https://api.github.com/users/yuchaojiang/repos","events_url":"https://api.github.com/users/yuchaojiang/events{/privacy}","received_events_url":"https://api.github.com/users/yuchaojiang/received_events","type":"User","site_admin":false},"created_at":"2018-05-17T11:38:58Z","updated_at":"2018-05-17T11:38:58Z","author_association":"OWNER","body":"This part of the code hasn't been updated in CODEX2 and we will do so ASAP. For now, can you use CODEX https://github.com/yuchaojiang/CODEX? Same section."}}
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