{"action":"created","issue":{"url":"https://api.github.com/repos/dpryan79/MethylDackel/issues/56","repository_url":"https://api.github.com/repos/dpryan79/MethylDackel","labels_url":"https://api.github.com/repos/dpryan79/MethylDackel/issues/56/labels{/name}","comments_url":"https://api.github.com/repos/dpryan79/MethylDackel/issues/56/comments","events_url":"https://api.github.com/repos/dpryan79/MethylDackel/issues/56/events","html_url":"https://github.com/dpryan79/MethylDackel/issues/56","id":301086730,"number":56,"title":"Methylation per read ","user":{"login":"nchernia","id":1417819,"avatar_url":"https://avatars0.githubusercontent.com/u/1417819?v=4","gravatar_id":"","url":"https://api.github.com/users/nchernia","html_url":"https://github.com/nchernia","followers_url":"https://api.github.com/users/nchernia/followers","following_url":"https://api.github.com/users/nchernia/following{/other_user}","gists_url":"https://api.github.com/users/nchernia/gists{/gist_id}","starred_url":"https://api.github.com/users/nchernia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nchernia/subscriptions","organizations_url":"https://api.github.com/users/nchernia/orgs","repos_url":"https://api.github.com/users/nchernia/repos","events_url":"https://api.github.com/users/nchernia/events{/privacy}","received_events_url":"https://api.github.com/users/nchernia/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2018-02-28T16:16:11Z","updated_at":"2018-04-27T20:40:41Z","closed_at":null,"author_association":"NONE","body":"Thank you for this tool - it's been really nice to work with (runs very fast and the code is very readable).\r\n\r\nWe are working on a project for which we need to know the methylation per read.  In Bismark, this is given via the XM tag, where there is essentially a string that represents (for every cytosine covered), the context and whether or not it is methylated.\r\n\r\nI'm currently getting this info by print out statements in lines 424-426 in extract.c and then processing the resulting text files but obviously this is less than ideal (multiple lines printed per read name that then need to be combined, files are big, etc).  Is there any way to make this an option in MethylDackel?  Alternatively, do you have suggestions for a better way to gather this info on a per read basis?\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/dpryan79/MethylDackel/issues/comments/385088191","html_url":"https://github.com/dpryan79/MethylDackel/issues/56#issuecomment-385088191","issue_url":"https://api.github.com/repos/dpryan79/MethylDackel/issues/56","id":385088191,"user":{"login":"nchernia","id":1417819,"avatar_url":"https://avatars0.githubusercontent.com/u/1417819?v=4","gravatar_id":"","url":"https://api.github.com/users/nchernia","html_url":"https://github.com/nchernia","followers_url":"https://api.github.com/users/nchernia/followers","following_url":"https://api.github.com/users/nchernia/following{/other_user}","gists_url":"https://api.github.com/users/nchernia/gists{/gist_id}","starred_url":"https://api.github.com/users/nchernia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nchernia/subscriptions","organizations_url":"https://api.github.com/users/nchernia/orgs","repos_url":"https://api.github.com/users/nchernia/repos","events_url":"https://api.github.com/users/nchernia/events{/privacy}","received_events_url":"https://api.github.com/users/nchernia/received_events","type":"User","site_admin":false},"created_at":"2018-04-27T20:40:41Z","updated_at":"2018-04-27T20:40:41Z","author_association":"NONE","body":"Yes, I should have clarified that I do see multiple instances, just double checking that I understood how it worked.  Yes, I need --ignoreFlags and --requireFlags though this isn't urgent."}}
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