{"action":"created","comment":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/29379754","id":29379754,"diff_hunk":"@@ -93,7 +154,19 @@ public void writeAlignment(final SAMRecord alignment) {\n         try {\n             out.write(alignment.getReadName());\n             out.write(FIELD_SEPARATOR);\n-            out.write(Integer.toString(alignment.getFlags()));\n+            switch (this.flagFieldsOutput) {","path":"src/java/htsjdk/samtools/SAMTextWriter.java","position":112,"original_position":112,"commit_id":"d7d0e3a117b8a6cbf04ecb3cb719102edec2fcd1","original_commit_id":"d7d0e3a117b8a6cbf04ecb3cb719102edec2fcd1","user":{"login":"mcovarr","id":10790523,"avatar_url":"https://avatars.githubusercontent.com/u/10790523?v=3","gravatar_id":"","url":"https://api.github.com/users/mcovarr","html_url":"https://github.com/mcovarr","followers_url":"https://api.github.com/users/mcovarr/followers","following_url":"https://api.github.com/users/mcovarr/following{/other_user}","gists_url":"https://api.github.com/users/mcovarr/gists{/gist_id}","starred_url":"https://api.github.com/users/mcovarr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcovarr/subscriptions","organizations_url":"https://api.github.com/users/mcovarr/orgs","repos_url":"https://api.github.com/users/mcovarr/repos","events_url":"https://api.github.com/users/mcovarr/events{/privacy}","received_events_url":"https://api.github.com/users/mcovarr/received_events","type":"User","site_admin":false},"body":"Warning: quite possibly more trouble than it's worth, but this could be converted to polymorphism in the enum instances:\r\n\r\n```\r\npublic enum FlagFieldsOutput {\r\n  ...\r\n  HEXADECIMAL {\r\n    @Override\r\n    public String format(int flags) {\r\n      return String.format(\"0x%x\", alignment.getFlags());\r\n    }\r\n    public abstract String format(int flags);\r\n  },\r\n  ...\r\n}\r\n```\r\n\r\nThen this code becomes:\r\n\r\n```\r\n  out.write(flagFieldsOutput.format(alignment.getFlags()));\r\n```","created_at":"2015-04-29T20:54:49Z","updated_at":"2015-04-29T20:54:49Z","html_url":"https://github.com/samtools/htsjdk/pull/232#discussion_r29379754","pull_request_url":"https://api.github.com/repos/samtools/htsjdk/pulls/232","_links":{"self":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/29379754"},"html":{"href":"https://github.com/samtools/htsjdk/pull/232#discussion_r29379754"},"pull_request":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/232"}}},"pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/232","id":34402830,"html_url":"https://github.com/samtools/htsjdk/pull/232","diff_url":"https://github.com/samtools/htsjdk/pull/232.diff","patch_url":"https://github.com/samtools/htsjdk/pull/232.patch","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/232","number":232,"state":"open","locked":false,"title":"Adding the ability to output the SAM flag field in various formats,","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"body":"similar to the 'samtools view -X' option.  Use the FLAG_FIELDS_OUTPUT\r\nwithin the Defaults class to set 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