{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/837","repository_url":"https://api.github.com/repos/samtools/htsjdk","labels_url":"https://api.github.com/repos/samtools/htsjdk/issues/837/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/837/comments","events_url":"https://api.github.com/repos/samtools/htsjdk/issues/837/events","html_url":"https://github.com/samtools/htsjdk/pull/837","id":218306286,"number":837,"title":"new Interface VCFIterator extends CloseableIterator<VariantContext>","user":{"login":"lindenb","id":33838,"avatar_url":"https://avatars0.githubusercontent.com/u/33838?v=4","gravatar_id":"","url":"https://api.github.com/users/lindenb","html_url":"https://github.com/lindenb","followers_url":"https://api.github.com/users/lindenb/followers","following_url":"https://api.github.com/users/lindenb/following{/other_user}","gists_url":"https://api.github.com/users/lindenb/gists{/gist_id}","starred_url":"https://api.github.com/users/lindenb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lindenb/subscriptions","organizations_url":"https://api.github.com/users/lindenb/orgs","repos_url":"https://api.github.com/users/lindenb/repos","events_url":"https://api.github.com/users/lindenb/events{/privacy}","received_events_url":"https://api.github.com/users/lindenb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"lindenb","id":33838,"avatar_url":"https://avatars0.githubusercontent.com/u/33838?v=4","gravatar_id":"","url":"https://api.github.com/users/lindenb","html_url":"https://github.com/lindenb","followers_url":"https://api.github.com/users/lindenb/followers","following_url":"https://api.github.com/users/lindenb/following{/other_user}","gists_url":"https://api.github.com/users/lindenb/gists{/gist_id}","starred_url":"https://api.github.com/users/lindenb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lindenb/subscriptions","organizations_url":"https://api.github.com/users/lindenb/orgs","repos_url":"https://api.github.com/users/lindenb/repos","events_url":"https://api.github.com/users/lindenb/events{/privacy}","received_events_url":"https://api.github.com/users/lindenb/received_events","type":"User","site_admin":false},"assignees":[{"login":"lindenb","id":33838,"avatar_url":"https://avatars0.githubusercontent.com/u/33838?v=4","gravatar_id":"","url":"https://api.github.com/users/lindenb","html_url":"https://github.com/lindenb","followers_url":"https://api.github.com/users/lindenb/followers","following_url":"https://api.github.com/users/lindenb/following{/other_user}","gists_url":"https://api.github.com/users/lindenb/gists{/gist_id}","starred_url":"https://api.github.com/users/lindenb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lindenb/subscriptions","organizations_url":"https://api.github.com/users/lindenb/orgs","repos_url":"https://api.github.com/users/lindenb/repos","events_url":"https://api.github.com/users/lindenb/events{/privacy}","received_events_url":"https://api.github.com/users/lindenb/received_events","type":"User","site_admin":false}],"milestone":null,"comments":15,"created_at":"2017-03-30T19:41:40Z","updated_at":"2017-09-21T17:47:34Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/837","html_url":"https://github.com/samtools/htsjdk/pull/837","diff_url":"https://github.com/samtools/htsjdk/pull/837.diff","patch_url":"https://github.com/samtools/htsjdk/pull/837.patch"},"body":"### Description\r\n\r\nAs far as I know, there is no existing solution to handle a VCF file from an InputStream like System.in.\r\nHere I introduce :\r\n+ VCFIterator an `Iterator<VariantContext>` with the method `VCFheader getFileHeader()`\r\n+ VCFIteratorBuilder a simple builder for the interface above (builds from uri,file and InputStream ). Decodes BCF,VCF, VCF.gz.\r\n\r\n\r\n```\r\n  VCFIterator r = new VCFIteratorBuilder().open(System.in);\r\n  while (r.hasNext()) {\r\n     System.out.println(r.next());\r\n  }\r\n  r.close();\r\n```\r\n```\r\n\r\n### Checklist\r\n\r\n- [X] Code compiles correctly\r\n- [X] New tests covering changes and new functionality\r\n- [X] All tests passing\r\n- [X] Extended the README / documentation, if necessary\r\n- [ ] Is not backward compatible (breaks binary or source compatibility)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/comments/331231149","html_url":"https://github.com/samtools/htsjdk/pull/837#issuecomment-331231149","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/837","id":331231149,"user":{"login":"lindenb","id":33838,"avatar_url":"https://avatars0.githubusercontent.com/u/33838?v=4","gravatar_id":"","url":"https://api.github.com/users/lindenb","html_url":"https://github.com/lindenb","followers_url":"https://api.github.com/users/lindenb/followers","following_url":"https://api.github.com/users/lindenb/following{/other_user}","gists_url":"https://api.github.com/users/lindenb/gists{/gist_id}","starred_url":"https://api.github.com/users/lindenb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lindenb/subscriptions","organizations_url":"https://api.github.com/users/lindenb/orgs","repos_url":"https://api.github.com/users/lindenb/repos","events_url":"https://api.github.com/users/lindenb/events{/privacy}","received_events_url":"https://api.github.com/users/lindenb/received_events","type":"User","site_admin":false},"created_at":"2017-09-21T17:47:34Z","updated_at":"2017-09-21T17:47:34Z","author_association":"CONTRIBUTOR","body":"@lbergelson @cmnbroad thank you for the reviews !\r\n\r\n- I've deprecated isGzippedSAMFile\r\n- created BCF2Codec.tryReadBCFVersion\r\n- fixed the typo\r\n- deleted FileBasedVCFIterator\r\n- used the codec.makeSourceFromStream\r\n- etc.."}}
{"actor":{"display_login":"lindenb"}}