{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/472","repository_url":"https://api.github.com/repos/samtools/htsjdk","labels_url":"https://api.github.com/repos/samtools/htsjdk/issues/472/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/472/comments","events_url":"https://api.github.com/repos/samtools/htsjdk/issues/472/events","html_url":"https://github.com/samtools/htsjdk/issues/472","id":133261519,"number":472,"title":"SAMFileWriterFactory doesn't use getDefaultCRAMReferenceSource","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/samtools/htsjdk/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/samtools/htsjdk/labels/cram","name":"cram","color":"eb6420"}],"state":"open","locked":false,"assignee":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2016-02-12T14:58:12Z","updated_at":"2016-03-28T13:54:48Z","closed_at":null,"body":"to navigate the reference fallback chain. Its called from the reader factory but not the writer factory. It should be called from SAMFileWriterFactory.createCRAMWriterWithSettings."},"comment":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/comments/202403780","html_url":"https://github.com/samtools/htsjdk/issues/472#issuecomment-202403780","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/472","id":202403780,"user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"created_at":"2016-03-28T13:54:48Z","updated_at":"2016-03-28T13:54:48Z","body":"Note that this change will break the picard SamFileConverter CRAM tests because the tests don't use a reference, but instead rely on the fact that the test file has only unmapped reads: https://github.com/broadinstitute/picard/blob/master/src/tests/java/picard/sam/SamFileConverterTest.java#L75."}}