{"action":"created","issue":{"url":"https://api.github.com/repos/smithlabcode/methpipe/issues/73","labels_url":"https://api.github.com/repos/smithlabcode/methpipe/issues/73/labels{/name}","comments_url":"https://api.github.com/repos/smithlabcode/methpipe/issues/73/comments","events_url":"https://api.github.com/repos/smithlabcode/methpipe/issues/73/events","html_url":"https://github.com/smithlabcode/methpipe/issues/73","id":96338397,"number":73,"title":"merge-methcounts \"inconsistent context\" errors","user":{"login":"cviner","id":10501947,"avatar_url":"https://avatars.githubusercontent.com/u/10501947?v=3","gravatar_id":"","url":"https://api.github.com/users/cviner","html_url":"https://github.com/cviner","followers_url":"https://api.github.com/users/cviner/followers","following_url":"https://api.github.com/users/cviner/following{/other_user}","gists_url":"https://api.github.com/users/cviner/gists{/gist_id}","starred_url":"https://api.github.com/users/cviner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cviner/subscriptions","organizations_url":"https://api.github.com/users/cviner/orgs","repos_url":"https://api.github.com/users/cviner/repos","events_url":"https://api.github.com/users/cviner/events{/privacy}","received_events_url":"https://api.github.com/users/cviner/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2015-07-21T14:56:08Z","updated_at":"2015-07-23T00:11:00Z","closed_at":null,"body":"I am running ```merge-methcounts``` to merge the output from ```methcounts``` (which was run for all genomic contexts, i.e. without ```-n```). However, I receive the fatal error: \"inconsistent context\" for all of my merge attempts.\r\n\r\nOne example line of my input file for which this error occurred is as follows:\r\n\r\n```\r\nchr1\t3000102\t-\tCHHx\t0\t0\r\n```\r\n\r\nAnother file had the error at the following line:\r\n```\r\nchr1\t3000417\t-\tCXGx\t0\t1\r\n```\r\n\r\nIt looks like this is caused by the terminal \"x\" in the genomic context column. What does this \"x\" mean and how can I resolve this problem?"},"comment":{"url":"https://api.github.com/repos/smithlabcode/methpipe/issues/comments/123912886","html_url":"https://github.com/smithlabcode/methpipe/issues/73#issuecomment-123912886","issue_url":"https://api.github.com/repos/smithlabcode/methpipe/issues/73","id":123912886,"user":{"login":"mengzhou","id":3333499,"avatar_url":"https://avatars.githubusercontent.com/u/3333499?v=3","gravatar_id":"","url":"https://api.github.com/users/mengzhou","html_url":"https://github.com/mengzhou","followers_url":"https://api.github.com/users/mengzhou/followers","following_url":"https://api.github.com/users/mengzhou/following{/other_user}","gists_url":"https://api.github.com/users/mengzhou/gists{/gist_id}","starred_url":"https://api.github.com/users/mengzhou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mengzhou/subscriptions","organizations_url":"https://api.github.com/users/mengzhou/orgs","repos_url":"https://api.github.com/users/mengzhou/repos","events_url":"https://api.github.com/users/mengzhou/events{/privacy}","received_events_url":"https://api.github.com/users/mengzhou/received_events","type":"User","site_admin":false},"created_at":"2015-07-23T00:11:00Z","updated_at":"2015-07-23T00:11:00Z","body":"can you paste that specific read here?"}}