{"action":"created","issue":{"url":"https://api.github.com/repos/bjpop/methpat/issues/24","repository_url":"https://api.github.com/repos/bjpop/methpat","labels_url":"https://api.github.com/repos/bjpop/methpat/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/bjpop/methpat/issues/24/comments","events_url":"https://api.github.com/repos/bjpop/methpat/issues/24/events","html_url":"https://github.com/bjpop/methpat/issues/24","id":170474996,"number":24,"title":"Possible to filter reads with partial coverage","user":{"login":"timp0","id":1441855,"avatar_url":"https://avatars.githubusercontent.com/u/1441855?v=3","gravatar_id":"","url":"https://api.github.com/users/timp0","html_url":"https://github.com/timp0","followers_url":"https://api.github.com/users/timp0/followers","following_url":"https://api.github.com/users/timp0/following{/other_user}","gists_url":"https://api.github.com/users/timp0/gists{/gist_id}","starred_url":"https://api.github.com/users/timp0/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timp0/subscriptions","organizations_url":"https://api.github.com/users/timp0/orgs","repos_url":"https://api.github.com/users/timp0/repos","events_url":"https://api.github.com/users/timp0/events{/privacy}","received_events_url":"https://api.github.com/users/timp0/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2016-08-10T17:37:28Z","updated_at":"2016-08-17T13:35:05Z","closed_at":null,"body":"Would it be possible to filter out reads with partial coverage - remove the reads that have \"unknown\" methylation status?  It'd be useful for high-coverage BS-seq data sets where we want to plot specific regional patterns."},"comment":{"url":"https://api.github.com/repos/bjpop/methpat/issues/comments/240412386","html_url":"https://github.com/bjpop/methpat/issues/24#issuecomment-240412386","issue_url":"https://api.github.com/repos/bjpop/methpat/issues/24","id":240412386,"user":{"login":"timp0","id":1441855,"avatar_url":"https://avatars.githubusercontent.com/u/1441855?v=3","gravatar_id":"","url":"https://api.github.com/users/timp0","html_url":"https://github.com/timp0","followers_url":"https://api.github.com/users/timp0/followers","following_url":"https://api.github.com/users/timp0/following{/other_user}","gists_url":"https://api.github.com/users/timp0/gists{/gist_id}","starred_url":"https://api.github.com/users/timp0/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timp0/subscriptions","organizations_url":"https://api.github.com/users/timp0/orgs","repos_url":"https://api.github.com/users/timp0/repos","events_url":"https://api.github.com/users/timp0/events{/privacy}","received_events_url":"https://api.github.com/users/timp0/received_events","type":"User","site_admin":false},"created_at":"2016-08-17T13:35:05Z","updated_at":"2016-08-17T13:35:05Z","body":"Tested - results in dropbox as *.pf.* two issues:\r\n\r\n1) Got a UTF-8 encode error from visualize.py, fixed by including a \"# -*- coding: utf-8 -*-\" line at the top of that code\r\n\r\n2) Larger issue, targreg3 in the OB strand doesn't show.  I know why - if you look at that in the full reads, you'll see that one of the reads has a CG that no other read has - at 1379.  This is not a real CG, it's generated by indels(or something) in the aligned read, and reported by bismark.  I've run into this before - Felix says it's intentional because a CG generated by a SNP should be reported.  As a result, all reads get filtered, because that read is missing a CG, and the other reads are all missing that 1379 CG.\r\n"}}
{"actor":{"display_login":"timp0"}}