{"action":"opened","issue":{"url":"https://api.github.com/repos/igvteam/igv/issues/335","repository_url":"https://api.github.com/repos/igvteam/igv","labels_url":"https://api.github.com/repos/igvteam/igv/issues/335/labels{/name}","comments_url":"https://api.github.com/repos/igvteam/igv/issues/335/comments","events_url":"https://api.github.com/repos/igvteam/igv/issues/335/events","html_url":"https://github.com/igvteam/igv/issues/335","id":194622712,"number":335,"title":"bisulfite mode in small letter reference sequences \"disabled\"","user":{"login":"aerval","id":9343181,"avatar_url":"https://avatars.githubusercontent.com/u/9343181?v=3","gravatar_id":"","url":"https://api.github.com/users/aerval","html_url":"https://github.com/aerval","followers_url":"https://api.github.com/users/aerval/followers","following_url":"https://api.github.com/users/aerval/following{/other_user}","gists_url":"https://api.github.com/users/aerval/gists{/gist_id}","starred_url":"https://api.github.com/users/aerval/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aerval/subscriptions","organizations_url":"https://api.github.com/users/aerval/orgs","repos_url":"https://api.github.com/users/aerval/repos","events_url":"https://api.github.com/users/aerval/events{/privacy}","received_events_url":"https://api.github.com/users/aerval/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-09T15:25:33Z","updated_at":"2016-12-09T15:25:33Z","closed_at":null,"body":"I am displaying WGBS data on the default mm10 genome that contains at some positions in the reference genome small letter bases (repeats etc.?) like ```act``` instead of ```ACT```. The default bisulfite mode does not highlight the methylation in reads in these areas. Similar, C highlighting does not highlight Cs etc. I assume its a bug because CpGs are recognized by capital CG letters?"}}
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