{"action":"created","issue":{"url":"https://api.github.com/repos/hhg7/defiant/issues/5","repository_url":"https://api.github.com/repos/hhg7/defiant","labels_url":"https://api.github.com/repos/hhg7/defiant/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/hhg7/defiant/issues/5/comments","events_url":"https://api.github.com/repos/hhg7/defiant/issues/5/events","html_url":"https://github.com/hhg7/defiant/issues/5","id":394358459,"node_id":"MDU6SXNzdWUzOTQzNTg0NTk=","number":5,"title":"Support for CGmap inputs","user":{"login":"harish0201","id":9093815,"node_id":"MDQ6VXNlcjkwOTM4MTU=","avatar_url":"https://avatars0.githubusercontent.com/u/9093815?v=4","gravatar_id":"","url":"https://api.github.com/users/harish0201","html_url":"https://github.com/harish0201","followers_url":"https://api.github.com/users/harish0201/followers","following_url":"https://api.github.com/users/harish0201/following{/other_user}","gists_url":"https://api.github.com/users/harish0201/gists{/gist_id}","starred_url":"https://api.github.com/users/harish0201/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/harish0201/subscriptions","organizations_url":"https://api.github.com/users/harish0201/orgs","repos_url":"https://api.github.com/users/harish0201/repos","events_url":"https://api.github.com/users/harish0201/events{/privacy}","received_events_url":"https://api.github.com/users/harish0201/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-12-27T10:33:23Z","updated_at":"2019-01-03T13:10:51Z","closed_at":null,"author_association":"NONE","body":"Hi Dave!\r\n\r\nI have recently come across cgmaptools which is a host of tools that can be used to call methylation and other analysis like allele specific methylation, snv calling etc. \r\n\r\nThe cgmap output can be derived from either post-processing the aligned bams or is one of the outputs from BS-Seeker. \r\n\r\nThe format as such looks like this:\r\n\r\n> chr1    G   3000851   CHH   CC  0.1   1   10\r\n> chr1    C   3001624   CHG   CA  0.0   0   9\r\n> chr1    C   3001631   CG    CG  1.0   5   5\r\n> chr1    G   3001632   CG    CG  0.9   9   10\r\n\r\nWhere the headers are: \r\n\r\nChromosome Reference_Nucleotide Position Context_Type Context Methylation_Status Methylated_Cyto_Counts Total_Cyto_Counts\r\n\r\nThe format as such seems to be similar to Bismark's format 5 as per the Readme. \r\n\r\nWould it be possible for you to support it? \r\n"},"comment":{"url":"https://api.github.com/repos/hhg7/defiant/issues/comments/451138603","html_url":"https://github.com/hhg7/defiant/issues/5#issuecomment-451138603","issue_url":"https://api.github.com/repos/hhg7/defiant/issues/5","id":451138603,"node_id":"MDEyOklzc3VlQ29tbWVudDQ1MTEzODYwMw==","user":{"login":"hhg7","id":17788973,"node_id":"MDQ6VXNlcjE3Nzg4OTcz","avatar_url":"https://avatars3.githubusercontent.com/u/17788973?v=4","gravatar_id":"","url":"https://api.github.com/users/hhg7","html_url":"https://github.com/hhg7","followers_url":"https://api.github.com/users/hhg7/followers","following_url":"https://api.github.com/users/hhg7/following{/other_user}","gists_url":"https://api.github.com/users/hhg7/gists{/gist_id}","starred_url":"https://api.github.com/users/hhg7/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hhg7/subscriptions","organizations_url":"https://api.github.com/users/hhg7/orgs","repos_url":"https://api.github.com/users/hhg7/repos","events_url":"https://api.github.com/users/hhg7/events{/privacy}","received_events_url":"https://api.github.com/users/hhg7/received_events","type":"User","site_admin":false},"created_at":"2019-01-03T13:10:51Z","updated_at":"2019-01-03T13:10:51Z","author_association":"OWNER","body":"Hi Harish,\r\n\r\nDefiant only reads regular ASCII files.  I've considered making it to read gz, but I don't know how yet. Please let me know how everything works out."}}
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