{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1175","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1175/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1175/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1175/events","html_url":"https://github.com/broadinstitute/gatk/issues/1175","id":118090690,"number":1175,"title":"SAM/BAM writers should always call setHeader on added records","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/broadinstitute/gatk/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/HTSJDK","name":"HTSJDK","color":"fbca04"}],"state":"open","locked":false,"assignee":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/gatk/milestones/5","html_url":"https://github.com/broadinstitute/gatk/milestones/alpha","labels_url":"https://api.github.com/repos/broadinstitute/gatk/milestones/5/labels","id":1220227,"number":5,"title":"alpha","description":"","creator":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"open_issues":16,"closed_issues":168,"state":"open","created_at":"2015-07-22T13:37:37Z","updated_at":"2015-12-03T17:19:24Z","due_on":"2015-12-04T05:00:00Z","closed_at":null},"comments":3,"created_at":"2015-11-20T17:46:52Z","updated_at":"2015-12-03T18:11:51Z","closed_at":null,"body":"This will ensure that the reference indices are properly resolved against the current SD before writing."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/161735671","html_url":"https://github.com/broadinstitute/gatk/issues/1175#issuecomment-161735671","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1175","id":161735671,"user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"created_at":"2015-12-03T18:11:51Z","updated_at":"2015-12-03T18:11:51Z","body":"I don't think \"the writer's header doesn't contain all the reference names in the records\" is a use case we want/need to support. Arguably we should throw an error in that case."}}