{"action":"opened","issue":{"url":"https://api.github.com/repos/samtools/hts-specs/issues/197","repository_url":"https://api.github.com/repos/samtools/hts-specs","labels_url":"https://api.github.com/repos/samtools/hts-specs/issues/197/labels{/name}","comments_url":"https://api.github.com/repos/samtools/hts-specs/issues/197/comments","events_url":"https://api.github.com/repos/samtools/hts-specs/issues/197/events","html_url":"https://github.com/samtools/hts-specs/issues/197","id":217404957,"number":197,"title":"SAM encoding and C-style definitions","user":{"login":"d-cameron","id":6036536,"avatar_url":"https://avatars0.githubusercontent.com/u/6036536?v=3","gravatar_id":"","url":"https://api.github.com/users/d-cameron","html_url":"https://github.com/d-cameron","followers_url":"https://api.github.com/users/d-cameron/followers","following_url":"https://api.github.com/users/d-cameron/following{/other_user}","gists_url":"https://api.github.com/users/d-cameron/gists{/gist_id}","starred_url":"https://api.github.com/users/d-cameron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/d-cameron/subscriptions","organizations_url":"https://api.github.com/users/d-cameron/orgs","repos_url":"https://api.github.com/users/d-cameron/repos","events_url":"https://api.github.com/users/d-cameron/events{/privacy}","received_events_url":"https://api.github.com/users/d-cameron/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-03-27T23:30:23Z","updated_at":"2017-03-27T23:30:23Z","closed_at":null,"body":"The SAM specifications do not define a file encoding. This is problematic as some \"ASCII\" encoding codepoints for punctuation that differ from \"US-ASCII\". This is extremely problematic as many of the Regex restrictions.\r\n\r\nFurthermore, the regex grammar used is not defined thus is ambiguous (see http://seqanswers.com/forums/showthread.php?p=205407#post205407 for context). Similarly, operators used in defining BAM headers are not explicitly defined.\r\n\r\nProposed resolution:\r\n\r\n- Define the file format as \"US-ASCII\"\r\n- Add introductory text that states that\r\n   - All regexes are POSIX basic regular expressions\r\n   - code and pseudo-code in the document should be interpreted as C\r\n"}}
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