{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/386","labels_url":"https://api.github.com/repos/samtools/htsjdk/issues/386/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/386/comments","events_url":"https://api.github.com/repos/samtools/htsjdk/issues/386/events","html_url":"https://github.com/samtools/htsjdk/pull/386","id":117012741,"number":386,"title":"A new comparator that produces an ordering of SAMRecords that effecti…","user":{"login":"tfenne","id":1609210,"avatar_url":"https://avatars.githubusercontent.com/u/1609210?v=3","gravatar_id":"","url":"https://api.github.com/users/tfenne","html_url":"https://github.com/tfenne","followers_url":"https://api.github.com/users/tfenne/followers","following_url":"https://api.github.com/users/tfenne/following{/other_user}","gists_url":"https://api.github.com/users/tfenne/gists{/gist_id}","starred_url":"https://api.github.com/users/tfenne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfenne/subscriptions","organizations_url":"https://api.github.com/users/tfenne/orgs","repos_url":"https://api.github.com/users/tfenne/repos","events_url":"https://api.github.com/users/tfenne/events{/privacy}","received_events_url":"https://api.github.com/users/tfenne/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-15T19:36:53Z","updated_at":"2015-11-15T19:39:39Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/386","html_url":"https://github.com/samtools/htsjdk/pull/386","diff_url":"https://github.com/samtools/htsjdk/pull/386.diff","patch_url":"https://github.com/samtools/htsjdk/pull/386.patch"},"body":"…vely yields SO=unsorted and GO=query using a sort on a hash of queryname."},"comment":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/comments/156846032","html_url":"https://github.com/samtools/htsjdk/pull/386#issuecomment-156846032","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/386","id":156846032,"user":{"login":"tfenne","id":1609210,"avatar_url":"https://avatars.githubusercontent.com/u/1609210?v=3","gravatar_id":"","url":"https://api.github.com/users/tfenne","html_url":"https://github.com/tfenne","followers_url":"https://api.github.com/users/tfenne/followers","following_url":"https://api.github.com/users/tfenne/following{/other_user}","gists_url":"https://api.github.com/users/tfenne/gists{/gist_id}","starred_url":"https://api.github.com/users/tfenne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfenne/subscriptions","organizations_url":"https://api.github.com/users/tfenne/orgs","repos_url":"https://api.github.com/users/tfenne/repos","events_url":"https://api.github.com/users/tfenne/events{/privacy}","received_events_url":"https://api.github.com/users/tfenne/received_events","type":"User","site_admin":false},"created_at":"2015-11-15T19:39:39Z","updated_at":"2015-11-15T19:39:39Z","body":"@yfarjoun, @nh13 : small PR here, could you take a look please and let me know what you think?  My goal is to provide a way to sort SAMRecords that will give every read for a template together, but otherwise in random order.  Motivated by the fact that the SRA has done some horrible things to 1KG BAMs (read name and mapping position seem highly correlated in at least one example I looked at).\r\n\r\nI was tempted to add this as a new SortOrder, so I could leverage it anywhere SAMRecord sorting is provided in Picard, but felt that wasn't ideal since I really want the `@HD` line to correctly report `SO=unsorted GO=query`.\r\n\r\nThoughts on whether this is the right way to do this?  If so, I'll add some basic tests and rebase."}}