{"action":"closed","issue":{"url":"https://api.github.com/repos/bioinformatics-core-shared-training/cruk-summer-school-2017/issues/2","repository_url":"https://api.github.com/repos/bioinformatics-core-shared-training/cruk-summer-school-2017","labels_url":"https://api.github.com/repos/bioinformatics-core-shared-training/cruk-summer-school-2017/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/bioinformatics-core-shared-training/cruk-summer-school-2017/issues/2/comments","events_url":"https://api.github.com/repos/bioinformatics-core-shared-training/cruk-summer-school-2017/issues/2/events","html_url":"https://github.com/bioinformatics-core-shared-training/cruk-summer-school-2017/issues/2","id":245331912,"number":2,"title":"naive genotyping example","user":{"login":"markdunning","id":3796277,"avatar_url":"https://avatars2.githubusercontent.com/u/3796277?v=4","gravatar_id":"","url":"https://api.github.com/users/markdunning","html_url":"https://github.com/markdunning","followers_url":"https://api.github.com/users/markdunning/followers","following_url":"https://api.github.com/users/markdunning/following{/other_user}","gists_url":"https://api.github.com/users/markdunning/gists{/gist_id}","starred_url":"https://api.github.com/users/markdunning/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/markdunning/subscriptions","organizations_url":"https://api.github.com/users/markdunning/orgs","repos_url":"https://api.github.com/users/markdunning/repos","events_url":"https://api.github.com/users/markdunning/events{/privacy}","received_events_url":"https://api.github.com/users/markdunning/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-07-25T09:01:58Z","updated_at":"2017-08-02T14:57:05Z","closed_at":"2017-08-02T14:57:05Z","body":"the getSeq function should be used on the baseSummary object, not the gene model\r\n\r\nrefSeq <- getSeq(hg19, renameSeqlevels(baseSummary, c(\"17\"=\"chr17\")))\r\nrefSeq\r\n\r\nmycalls==refSeq\r\n\r\nbaseSummary[mycalls != refSeq & meta$depth > 10]"}}
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